Genome-Wide Mapping of SNPs
in Non-coding RNAs
Shangwei Ning and Yunpeng Zhang
Abstract
Non-coding RNAs (ncRNAs) are essential
players that participate in multiple cellular pro-
cesses. Cumulative evidence has linked
ncRNA-related single nucleotide
polymorphisms (SNPs) to various human
diseases. However, the knowledge of
ncRNA-related SNPs and their potential func-
tional mechanisms in human disease need to
be further discovered. Here, we reviewed
related studies on functional SNPs in two
main types of ncRNA, microRNAs (miRNAs)
and long non-coding RNAs (lncRNAs), with a
particular focus on these ncRNA-related SNPs
as novel risk factor of disease etiology. These
studies will gain global insights into the rela-
tionship between ncRNAs and their functions.
Keywords
miRNA · lncRNA · Disease · Single nucleotide
polymorphisms (SNPs)
5.1 Introduction
Dissecting the characters of genetic variants in
human disease is currently the subject of intense
S. Ning (*) · Y. Zhang (*)
College of Bioinformatics Science and Technology,
Harbin Medical University, Harbin, China
e-mail: ningsw@ems.hrbmu.edu.cn;
zhangyp@hrbmu.edu.cn
# Springer Nature Singapore Pte Ltd. 2018
X. Li et al. (eds.), Non-coding RNAs in Complex Diseases, Advances in Experimental Medicine and
Biology 1094, https://doi.org/10.1007/978-981-13-0719-5_5
5
research [1]. The most common variants are
single-nucleotide polymorphisms (SNPs), which
have been used as biomarkers of disease associa-
tion and susceptibility. SNPs within coding
regions can affect protein functions directly by
changing the amino acid sequences or by
disrupting their regulations. Once the SNPs
occur in the sequence of non-coding RNA, they
may perform their functions at different
mechanisms.
Currently, human SNPs in microRNAs and the
microRNA target sites have been widely
investigated. MicroRNAs (miRNAs) represent a
widely existed small non-coding RNAs that exert
their function by target to the 30 -untranslated
regions of mRNAs (30 -UTR), resulting in
mRNA degradation or translational repression
[2]. The role of miRNA polymorphisms in
human disease pathogenesis has been well
established in both experimental and bioinformat-
ics evidence [3, 4]. With the increasing number of
related researches annually, the underlying mech-
anism of miRNA associated SNPs in human
diseases will be discovered deeply, and open a
novel blueprint for disease treatment.
In the meantime, our knowledge of another
type of non-coding RNA, long non-coding
RNAs (lncRNAs) has been expanded with
remarkable speed, which revealed unexpected
function for these molecules [5]. lncRNAs are a
class of extensively transcribed non-coding RNA
molecules in the mammalian genome, which are
39
40
usually greater than 200 nt in length [6]. Recent
studies have shown that lncRNAs are involved in
diverse biological functions, such as epigenetic
regulation [7], cell cycle control and apoptosis
[8], reprogramming and pluripotency [9] and
gene expression regulation [10]. Moreover,
emerging studies have revealed that significant
numbers of lncRNAs are associated with human
diseases, including breast cancer [11], prostate
cancer [12], leukemias [13] and nervous system
diseases [14]. Although the importance of
lncRNAs in human diseases has been recognized,
the specific elements with functional significance
in the lncRNA sequences remain largely uniden-
tified. Some vital genetic variants in lncRNAs
may bring new discovery for lncRNAs, which
will be beneficial for disease related findings
[15]. Currently, several lncRNA polymorphisms
have been found to be involved in human diseases
progression. For example, SNPs in a lncRNA
called ANRIL have been related with an
increased risk of atherosclerosis, type 2 diabetes,
coronary heart disease and several cancers
[16]. Thus, lncRNA associated genetic
polymorphisms are potential candidates for
human disease, and are critical factors for clinical
and biology researches.
5.2 Mapping SNPs in Human
miRNA Targets
MiRNAs are known to regulate gene expression
through post-transcription regulation mechanism
by binding to target sites [17]. Recent studies
have demonstrated that this binding can be
inhibited by mutations in the miRNA target
sites; this class of single nucleotide
polymorphisms (SNPs) likely acts as a switch in
the 30 -UTR to eliminate an existing miRNA reg-
ulation or to create new target sites [3, 18, 19],
which are associated with many human cancers,
such as lung cancer, colon cancer and breast
cancer [20–24]. Therefore, naturally occurring
SNPs in putative miRNA target sites (tarSNPs)
are potentially functional variations that may be
implicated in important biological processes or
cancer. Several studies have analysed human
S. Ning and Y. Zhang
polymorphisms and identified the SNPs that are
predicted to reside in miRNA target sites, such as
dbSMR [25], Patrocles [26], PolymiRTS [27] and
MicroSNiPer [28]. However, two challenging
issues remain to be addressed. First, how can we
systematically evaluate the risk of candidate
tarSNPs in a specific human disease? Second,
how do we use these results to identify disease-
causing mechanisms?
To address these challenges, computational
prioritization of candidate tarSNPs prior to exper-
imental analysis is both necessary and valuable
and will provide a guide for the interpretation of
successful biological experiments. In addition,
the determination of potential risk tarSNPs may
result in the identification of new disease-
associated genes and provide novel insights into
the cellular mechanisms that underlie various
diseases. With the advent of high-throughput
technologies, large-scale disease genomic data
have been generated. One way that these
biological data can be used is to prioritize candi-
date genes based on the integration of different
data sources [29, 30], which suggests that novel
methods that use current biological knowledge to
prioritize tarSNPs can be developed.
A tarSNP is usually defined as a typical triplet
that requires a complex interaction between three
items: the SNP, the miRNA and the target
mRNA. The major challenge is to precisely eval-
uate the extent of the risk of these ‘interactions’
based on different data sources. A recent experi-
mental study found that risk SNPs associated with
breast cancer can affect an individual’s cancer
susceptibility by disrupting miRNA target sites
[31], which indicates that known risk SNPs or
SNPs that reside in disease-associated genes and
major regulatory genes may be potential risk
tarSNPs. For example, a SNP (rs4245739) in the
30 -UTR of MDM4, which is a critical negative
regulator of P53, was recently associated with
ovarian cancer progression because of its effect
on P53 expression [32]. Based on this informa-
tion, a tarSNP should have greater risk-
prioritization weight if its related items (SNP,
miRNA or target mRNA) are involved in cancer
pathways or key biological processes. Moreover,
several similar studies have shown that tarSNPs
5 Identification of SNPs in Non-coding RNAs
Fig. 5.1 A computational strategy for identifying disease candidate tarSNPs
that affect cancer risk may be widespread [33, 34]
and that a large number of risk tarSNPs have yet
to be discovered. A computational strategy can be
used to prioritize tarSNPs and search for risk
tarSNPs (Fig. 5.1). In the first step of this strategy,
candidate tarSNPs are classified as such if they
can disrupt existing miRNA regulation or create
new target sites. In the second step, each tarSNP
is assigned a score based on different individual
biological sources. These data sources including:
protein-protein interactions, known disease gene
set, SNP conservation information, SNP potential
regulatory information and SNP linkage disequi-
librium (LD) information. Then, these
SNP-related sources were integrated to generate
a single score based on an integrated algorithm,
such as SPOT [35]. In the third step, these candi-
date tarSNPs are ranked based on the scores
generated in the second step. Finally, the rankings
from the separate data sources are integrated into
a single ranking that provides an overall score for
each tarSNP. Candidate tarSNPs were prioritized
based on the overall score, and the rank position
reflects the relevance to a specific cancer. Candi-
date tarSNPs are ranked according to their disease
relevance based on their functional genomic con-
text. In summary, recognition of risk tarSNPs and
identification of the regulatory mechanism is the
first step towards developing a better understand-
ing of miRNAs in complex cellular systems.
41
Identifying the risk tarSNPs that are associated
with specific diseases from the large number of
candidate tarSNPs by biological experimentation
is laborious and time consuming. We can develop
some useful computational methods which are
suited for specific biological problems, and pro-
vide a general guideline for functions and
mechanisms of tarSNPs in human disease.
5.3 Mapping Disease-Associated
SNPs in lncRNAs
Genome-Wide Association Studies (GWAS)
have identified a large number of phenotype-
associated SNPs in intergenic regions of the
human genome, it is difficult to explain the path-
ogenesis of these SNPs, because they do not
result in changes in protein content. Recent stud-
ies are beginning to link these risk SNPs to
lncRNAs. For example, a meta-analysis of two
existing GWAS found prostate cancer-associated
SNPs in lncRNA regions [36]. The correlation
between phenotype related SNPs and lncRNA-
mediated regulation will provide independent
support for the effect of lncRNA, and make peo-
ple have a better understanding of the pathogene-
sis of disease. A previous study researched
whether previously published phenotype related
SNPs could be involved in lncRNA-mediated
42
Fig. 5.2 The global map of the phenotype-associated SNPs in human lincRNAs. (Ning et al. [37])
regulation.They found 217 phenotype-associated
SNPs located in 162 lncRNAs, which were
associated with 116 phenotypes [37]. Especially,
there were “Psychiatric” class and “Neurological”
respectively including 28 and 16 phenotype-
associated lncRNAs. This finding was consistent
with previous studies, which revealed that
lncRNAs played important roles in brain [38]
and neuropsychiatric disorders [14]. They also
found 27, 26 and 18 SNPs in “Endocrine” class.
“Cardiovascular” class and “Cancer” class,
respectively. These results were also consistent
with previous studies [15]. Finally, this study
constructed a circular map to gain a global view
of the phenotype-associated SNPs in each human
lncRNA and other information, and found that
some lncRNAs contained multiple SNPs that
were associated with particular diseases,
suggesting that these lncRNAs might play key
poles in these diseases (Fig. 5.2). For instance,
they found four bipolar disorder SNPs in one
S. Ning and Y. Zhang
lncRNA on chromosome 1; the functional impor-
tance of lncRNA proved by both the density of
SNP and the proportion of evolutionarily
conserved region (ECR) length, rs472913, one
disease-associated SNP [39], had a influence
upon secondary structure of RNA. They found
four type 2 diabetes risk SNPs in a lncRNA on
chromosome 5. Two SNPs in this lncRNA,
rs7590866 and rs980229 [40], despite lncRNA
had a fairly low degree of conservation, had a
great influence upon RNA secondary structures.
Furthermore, they found three of five type 1 dia-
betes risk SNPs in a lncRNA on chromosome
12, rs2106406, rs2106407 and rs12425190 [41],
had great influence upon RNA secondary
structures. They also found that a few SNPs in
human lncRNAs were associated with breast and
prostate cancer. These SNPs were located in low
SNP density and evolutionarily conserved
lncRNAs and some of these SNPs could affect
RNA secondary structures significantly. In
5 Identification of SNPs in Non-coding RNAs
summary, more SNPs located in lncRNAs and
their potential functional and etiologic
significances would be identified in the future,
which can be candidate causal SNPs for diseases.
5.4 Identification of SNPs’ Effects
on lncRNA Structure
Some studies focused on evaluating the effects of
lncRNA-related SNPs on RNA secondary
structures. Because of uncertainty of the exact
function of most lncRNA sequences, it is hard
to determine the cause of the disease related SNPs
in the lncRNA molecule. Previous studies have
shown that functional non-coding regions in the
human genome had conserved RNA secondary
structures [42], and certain human diseases
could be caused by variants inducing structural
changes [26], suggesting RNA structural change
as a potential molecular cause of the disease.
To investigate the effects of lncRNA
polymorphisms on RNA secondary structures, a
recent study computed the minimum free energy
(MFE, ΔG) changes caused by SNPs in human
lncRNAs [37]. For quantitatively evaluating the
RNA structural changes caused by each lncRNA
polymorphism’s mutant and wild-type alleles, and
they extracted 200 bp flanking sequences on both
sides of SNP. Then, they assessed the minimum free
energy (MFE, ΔG) based on the 401 bp sequences
using the RNA Fold program [42]. RNA structural
changes (ΔΔG) were calculated by the MFE
differences using ΔΔG ¼ j ΔGmut  ΔGwtj,
where ΔGmut was the MFE of the mutant-type
allele, and ΔGwt was the MFE of the wild-type
allele. Furthermore, they used a significance calcula-
tion to search for the large structural changes caused
by SNPs [43]. They computed a P-value for each
lncRNA polymorphism, which was based on the
total number of SNPs in a lncRNA divided by the
rank of the SNP’s MFE change in this lncRNA.
They found that most lncRNA polymorphisms had
only small effects on RNA secondary structures
(Fig. 5.3). A small number of SNPs, however, had
a large effect, suggesting that these SNPs might play
important roles on lncRNA function and disease.
Therefore, they next identified significant structural
changes through quantitative calculations. Based on
43
the P-value of 0.1, they classified the top 10% of
lncRNA polymorphisms that had large influence
upon RNA secondary structures. A striking increase
of ΔΔG values was observed in these SNPs, in
particular in the ΔΔG values >3 kcal/mol. They
further investigated whether these significant SNPs
had an enrichment trend in ECRs. For all SNPs in
lncRNAs, there were 1.99% of SNPs located in
ECRs, but for significant SNPs, this fraction rose to
2.08% (P ¼ 0.154, chi-square test), especially in
these SNPs that had particularly large effects on
RNA secondary structures (6  ΔΔG 7), the
fraction rose to 2.53%, and this enrichment was
significant (P ¼ 0.029, chi-square test). The conse-
quence of RNA structural changes of lncRNA might
exhibit their functional effects, even contributing to
disease. For instance, they found a SNP, rs9858061,
located in an ECR of a low SNP density lncRNA
region (6.87 SNPs/kb) on chromosome 3. The MFE
change (ΔΔG) between G-allele and U-allele was
6 kcal/mol. This SNP had a very high LD relation-
ship with a disease-risk SNP for type 2 diabetes
(rs9290240) in the same lncRNA [44], proving that
rs9858061 might be candidate disease-risk SNP for
type 2 diabetes.
In summary, some known disease-associated
SNPs located in the region of lncRNAs had sig-
nificant effects on RNA secondary structures,
which might have causal effects on disease risk.
5.5 Mapping Disease-Associated
SNPs in lncRNA TFBSs
Previous studies have mentioned that SNPs in
transcription factor binding sites (TFBSs) of
protein-coding genes could affect gene expres-
sion by changing transcription factor binding
ability, and thus participated in human diseases
[45–49]. A recent study on a tumor suppressor
lncRNA (PTCSC3) has also proved that SNP
rs944289 could enhance papillary thyroid carci-
noma sensitivity by dysregulating lncRNA
expression through decreasing the binding activ-
ity of both C/EBPα and C/EBPβ [50]. Therefore,
as a regulator in the human lncRNA TFBSs,
SNPs may impact the binding of transcription
factor, resulting in the difference of lncRNA
expression level and, potentially, pathopoiesia.
44
Fig. 5.3 Structural effects of lncRNA-related SNPs. (Ning et al. [37])
To provide a helpful annotation of these poten-
tial functional variants, SNP@lincTFBS database
was designed for integrating and annotating func-
tional SNPs in predicted lncRNA TFBSs
(Fig. 5.4) [51]. In total, 6665 SNPs were
identified happening in 6614 TFBSs of 2423
human lncRNAs, and a useful and intergrated
resource of candidate SNPs related to the abnor-
mal expression of lncRNAs was provided. 4331
human lncRNAs with genomic coordinates from
the lncRNA list of GENCODE project (version
16) were obtained [52], and lncRNAs without
unique determinate chromosomal location were
removed. 5 kb upstream to 1 kb downstream
region of the start site of each lncRNA was
regarded as its promoter region consulted by pre-
vious research [53]. After that, TFBSs of human
lncRNAs in these regions were predicted and they
computed the scores and threshold using the
S. Ning and Y. Zhang
TransFac Matrix Database (v7.0) from Biobase
[54]. As a consequence, 33181 TFBSs were
predicted in connection with 3839 human
lncRNAs based on defined promoter regions of
lncRNA. In addition, SNPs were downloaded in
the open source dbSNP database (build version
137) and 6665 SNPs were identified within 6614
presumptive human TFBSs of 2423 lncRNAs.
SNP@lincTFBS allows researchers to execute
SNP and TFBS searches in human lncRNAs.
SNP@lincTFBS contains 8300 entries of
annotated SNP-TFBS-lncRNA associations,
including 5835 lncRNAs, 33181 TFBSs, 6665
SNPs and 165 transcription factors.
SNP@lincTFBS predicted a large number of
TFBSs in the promoter regions of human
lncRNAs and found that the distribution of
SNPs in the lncRNA TFBSs was extensive. Pre-
vious studies have proved that each transcription
5 Identification of SNPs in Non-coding RNAs
Fig. 5.4 Architecture of SNP@lincTFBS. (Ning et al. [51])
factor can bind to several TFBSs in the promoter
regions of protein-coding genes, thus controlling
the transcription of genetic information from
DNA to messenger RNA. It has a similar phe-
nomenon in huamn lncRNA and a transcription
factor have the ability to bind to many lncRNA
TFBSs (~247 lncRNA), whereas ~20 TFBSs that
have been identified SNPs within them, and every
5.3 TFBSs had a SNP for each transcription fac-
tor. Besides, they discovered that high
frequencies of SNPs located in the region of
lncRNA TFBSs around lncRNA start site,
45
indicating that these SNPs within lncRNA
TFBSs might affect the expression of lncRNAs
tremendously. In summary, promoter regions of
most human lncRNAs have TFBSs and the distri-
bution of SNPs in these lncRNAs TFBSs is wide-
spread. It will be very useful to establish a
database that provides genomic informations
and annotations of SNPs in the TFBSs of pre-
sumptive promoter regions of human lncRNAs,
and this data has the potential to become an
available resource for further studies of lncRNA
function and complex diseases.
46
5.6 Perspectives and Conclusion
In brief, the properties of miRNA and lncRNA-
related SNPs have been dissected by several pre-
vious studies from the perspective of human dis-
ease. At present, although abnormal expression of
many miRNA and lncRNAs detected in human
diseases, there is still deficient assertive interpre-
tation of their contribution to occurrence of
diseases. Many studies suggested that there were
important links between miRNA/lncRNA
polymorphisms and human diseases, albeit
vague etiology. In years to come, more
researchers will and should be carried out to
deeply interpret the effects of variants on
miRNA and lncRNA function and their direct
connection to diseases.
References
1. Freimer NB, Sabatti C (2007) Human genetics:
variants in common diseases. Nature 445
(7130):828–830
2. Bartel DP (2009) MicroRNAs: target recognition and
regulatory functions. Cell 136(2):215–233
3. Sethupathy P, Collins FS (2008) MicroRNA target site
polymorphisms and human disease. Trends Genet 24
(10):489–497
4. Ryan BM, Robles AI, Harris CC (2010) Genetic vari-
ation in microRNA networks: the implications for
cancer research. Nat Rev Cancer 10(6):389–402
5. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-
Vega B, Regev A, Rinn JL (2011) Integrative annota-
tion of human large intergenic noncoding RNAs
reveals global properties and specific subclasses.
Genes Dev 25(18):1915–1927
6. Ponting CP, Oliver PL, Reik W (2009) Evolution and
functions of long noncoding RNAs. Cell 136
(4):629–641
7. Nagano T, Mitchell JA, Sanz LA, Pauler FM,
Ferguson-Smith AC, Feil R, Fraser P (2008) The air
noncoding RNA epigenetically silences transcription
by targeting G9a to chromatin. Science 322
(5908):1717–1720
8. Huarte M, Guttman M, Feldser D, Garber M, Koziol
MJ, Kenzelmann-Broz D, Khalil AM, Zuk O, Amit I,
Rabani M et al (2010) A large intergenic noncoding
RNA induced by p53 mediates global gene repression
in the p53 response. Cell 142(3):409–419
9. Loewer S, Cabili MN, Guttman M, Loh YH,
Thomas K, Park IH, Garber M, Curran M, Onder T,
Agarwal S et al (2010) Large intergenic non-coding
RNA-RoR modulates reprogramming of human
S. Ning and Y. Zhang
induced pluripotent stem cells. Nat Genet 42
(12):1113–1117
10. Khalil AM, Guttman M, Huarte M, Garber M, Raj A,
Rivea Morales D, Thomas K, Presser A, Bernstein BE,
van Oudenaarden A et al (2009) Many human large
intergenic noncoding RNAs associate with chromatin-
modifying complexes and affect gene expression. Proc
Natl Acad Sci U S A 106(28):11667–11672
11. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM,
Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL et al
(2010) Long non-coding RNA HOTAIR reprograms
chromatin state to promote cancer metastasis. Nature
464(7291):1071–1076
12. Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM,
Cao Q, Brenner JC, Laxman B, Asangani IA, Grasso
CS, Kominsky HD et al (2011) Transcriptome
sequencing across a prostate cancer cohort identifies
PCAT-1, an unannotated lincRNA implicated in dis-
ease progression. Nat Biotechnol 29(8):742–749
13. Calin GA, Liu CG, Ferracin M, Hyslop T, Spizzo R,
Sevignani C, Fabbri M, Cimmino A, Lee EJ, Wojcik
SE et al (2007) Ultraconserved regions encoding
ncRNAs are altered in human leukemias and
carcinomas. Cancer Cell 12(3):215–229
14. Qureshi IA, Mattick JS, Mehler MF (2010) Long
non-coding RNAs in nervous system function and
disease. Brain Res 1338:20–35
15. Wapinski O, Chang HY (2011) Long noncoding
RNAs and human disease. Trends Cell Biol 21
(6):354–361
16. Pasmant E, Sabbagh A, Vidaud M, Bieche I (2010)
ANRIL, a long, noncoding RNA, is an unexpected
major hotspot in GWAS. FASEB J 25(2):444–448
17. Brennecke J, Stark A, Russell RB, Cohen SM (2005)
Principles of microRNA-target recognition. PLoS Biol
3(3):e85
18. Saunders MA, Liang H, Li WH (2007) Human poly-
morphism at microRNAs and microRNA target sites.
Proc Natl Acad Sci U S A 104(9):3300–3305
19. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X,
Bibe B, Bouix J, Caiment F, Elsen JM, Eychenne F
et al (2006) A mutation creating a potential illegitimate
microRNA target site in the myostatin gene affects
muscularity in sheep. Nat Genet 38(7):813–818
20. Chin LJ, Ratner E, Leng S, Zhai R, Nallur S, Babar I,
Muller RU, Straka E, Su L, Burki EA et al (2008) A
SNP in a let-7 microRNA complementary site in the
KRAS 30 untranslated region increases non-small cell
lung cancer risk. Cancer Res 68(20):8535–8540
21. Landi D, Gemignani F, Naccarati A, Pardini B,
Vodicka P, Vodickova L, Novotny J, Forsti A,
Hemminki K, Canzian F et al (2008) Polymorphisms
within micro-RNA-binding sites and risk of sporadic
colorectal cancer. Carcinogenesis 29(3):579–584
22. Saetrom P, Biesinger J, Li SM, Smith D, Thomas LF,
Majzoub K, Rivas GE, Alluin J, Rossi JJ, Krontiris TG
et al (2009) A risk variant in an miR-125b binding site
in BMPR1B is associated with breast cancer pathogen-
esis. Cancer Res 69(18):7459–7465
5 Identification of SNPs in Non-coding RNAs
23. Song F, Zheng H, Liu B, Wei S, Dai H, Zhang L, Calin
GA, Hao X, Wei Q, Zhang W et al (2009) An
miR-502-binding site single-nucleotide polymorphism
in the 30 -untranslated region of the SET8 gene is
associated with early age of breast cancer onset. Clin
Cancer Res 15(19):6292–6300
24. Tchatchou S, Jung A, Hemminki K, Sutter C,
Wappenschmidt B, Bugert P, Weber BH,
Niederacher D, Arnold N, Varon-Mateeva R et al
(2009) A variant affecting a putative miRNA target
site in estrogen receptor (ESR) 1 is associated with
breast cancer risk in premenopausal women. Carcino-
genesis 30(1):59–64
25. Hariharan M, Scaria V, Brahmachari SK (2009)
dbSMR: a novel resource of genome-wide SNPs
affecting microRNA mediated regulation. BMC Bio-
informatics 10:108
26. Hiard S, Charlier C, Coppieters W, Georges M,
Baurain D (2010) Patrocles: a database of polymorphic
miRNA-mediated gene regulation in vertebrates.
Nucleic Acids Res 38(Database issue):D640–D651
27. Bao L, Zhou M, Wu L, Lu L, Goldowitz D, Williams
RW, Cui Y (2007) PolymiRTS database: linking
polymorphisms in microRNA target sites with com-
plex traits. Nucleic Acids Res 35(Database issue):
D51–D54
28. Barenboim M, Zoltick BJ, Guo Y, Weinberger DR
(2010) MicroSNiPer: a web tool for prediction of
SNP effects on putative microRNA targets. Hum
Mutat 31(11):1223–1232
29. Aerts S, Lambrechts D, Maity S, Van Loo P,
Coessens B, De Smet F, Tranchevent LC, De
Moor B, Marynen P, Hassan B et al (2006) Gene
prioritization through genomic data fusion. Nat
Biotechnol 24(5):537–544
30. Wu X, Jiang R, Zhang MQ, Li S (2008) Network-
based global inference of human disease genes. Mol
Syst Biol 4:189
31. Nicoloso MS, Sun H, Spizzo R, Kim H,
Wickramasinghe P, Shimizu M, Wojcik SE, Ferdin J,
Kunej T, Xiao L et al (2010) Single-nucleotide
polymorphisms inside microRNA target sites influ-
ence tumor susceptibility. Cancer Res 70
(7):2789–2798
32. Wynendaele J, Bohnke A, Leucci E, Nielsen SJ,
Lambertz I, Hammer S, Sbrzesny N, Kubitza D,
Wolf A, Gradhand E et al (2010) An illegitimate
microRNA target site within the 30 UTR of MDM4
affects ovarian cancer progression and chemosen-
sitivity. Cancer Res 70(23):9641–9649
33. Liang D, Meyer L, Chang DW, Lin J, Pu X, Ye Y,
Gu J, Wu X, Lu K (2010) Genetic variants in
MicroRNA biosynthesis pathways and binding sites
modify ovarian cancer risk, survival, and treatment
response. Cancer Res 70(23):9765–9776
34. Kontorovich T, Levy A, Korostishevsky M, Nir U,
Friedman E (2010) Single nucleotide polymorphisms
in miRNA binding sites and miRNA genes as breast/
47
ovarian cancer risk modifiers in Jewish high-risk
women. Int J Cancer 127(3):589–597
35. Saccone SF, Bolze R, Thomas P, Quan J, Mehta G,
Deelman E, Tischfield JA, Rice JP (2010) SPOT: a
web-based tool for using biological databases to prior-
itize SNPs after a genome-wide association study.
Nucleic Acids Res 38(Web Server issue):W201–
W209
36. Jin G, Sun J, Isaacs SD, Wiley KE, Kim ST, Chu LW,
Zhang Z, Zhao H, Zheng SL, Isaacs WB et al (2011)
Human polymorphisms at long non-coding RNAs
(lncRNAs) and association with prostate cancer risk.
Carcinogenesis 32(11):1655–1659
37. Ning S, Wang P, Ye J, Li X, Li R, Zhao Z, Huo X,
Wang L, Li F, Li X (2013) A global map for dissecting
phenotypic variants in human lincRNAs. Eur J Hum
Genet 21(10):1128–1133
38. Mercer TR, Dinger ME, Sunkin SM, Mehler MF,
Mattick JS (2008) Specific expression of long noncod-
ing RNAs in the mouse brain. Proc Natl Acad Sci U S
A 105(2):716–721
39. Scott LJ, Muglia P, Kong XQ, Guan W, Flickinger M,
Upmanyu R, Tozzi F, Li JZ, Burmeister M, Absher D
et al (2009) Genome-wide association and meta-
analysis of bipolar disorder in individuals of
European ancestry. Proc Natl Acad Sci U S A 106
(18):7501–7506
40. Saxena R, Voight BF, Lyssenko V, Burtt NP, de
Bakker PI, Chen H, Roix JJ, Kathiresan S, Hirschhorn
JN, Daly MJ et al (2007) Genome-wide association
analysis identifies loci for type 2 diabetes and triglyc-
eride levels. Science 316(5829):1331–1336
41. Consortium TWTCC (2007) Genome-wide associa-
tion study of 14,000 cases of seven common diseases
and 3,000 shared controls. Nature 447(7145):661–678
42. Hofacker IL (2003) Vienna RNA secondary structure
server. Nucleic Acids Res 31(13):3429–3431
43. Halvorsen M, Martin JS, Broadaway S, Laederach A
(2010) Disease-associated mutations that alter the
RNA structural ensemble. PLoS Genet 6(8):e1001074
44. Sladek R, Rocheleau G, Rung J, Dina C, Shen L,
Serre D, Boutin P, Vincent D, Belisle A, Hadjadj S
et al (2007) A genome-wide association study
identifies novel risk loci for type 2 diabetes. Nature
445(7130):881–885
45. Hata J, Matsuda K, Ninomiya T, Yonemoto K,
Matsushita T, Ohnishi Y, Saito S, Kitazono T,
Ibayashi S, Iida M et al (2007) Functional SNP in an
Sp1-binding site of AGTRL1 gene is associated with
susceptibility to brain infarction. Hum Mol Genet 16
(6):630–639
46. Blanton SH, Burt A, Garcia E, Mulliken JB, Stal S,
Hecht JT (2010) Ethnic heterogeneity of IRF6 AP-2a
binding site promoter SNP association with
nonsyndromic cleft lip and palate. Cleft Palate
Craniofac J 47(6):574–577
47. Badano I, Stietz SM, Schurr TG, Picconi AM,
Fekete D, Quintero IM, Cabrera MD, Campos RH,
Liotta JD (2012) Analysis of TNFalpha promoter
48
SNPs and the risk of cervical cancer in urban
populations of Posadas (Misiones, Argentina). J Clin
Virol 53(1):54–59
48. Jung M, Cho BC, Lee CH, Park HS, Kang YA, Kim
SK, Chang J, Kim DJ, Rha SY, Kim JH et al (2012)
EGFR polymorphism as a predictor of clinical out-
come in advanced lung cancer patients treated with
EGFR-TKI. Yonsei Med J 53(6):1128–1135
49. Kohanbash G, Ishikawa E, Fujita M, Ikeura M,
McKaveney K, Zhu J, Sakaki M, Sarkar SN, Okada
H (2012) Differential activity of interferon-alpha8 pro-
moter is regulated by Oct-1 and a SNP that dictates
prognosis of glioma. Oncoimmunology 1(4):487–492
50. Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J,
Liyanarachchi S, Davuluri RV, Nagy R, de la Chapelle
A (2012) The polymorphism rs944289 predisposes to
papillary thyroid carcinoma through a large intergenic
noncoding RNA gene of tumor suppressor type. Proc
Natl Acad Sci U S A 109(22):8646–8651
S. Ning and Y. Zhang
51. Ning S, Zhao Z, Ye J, Wang P, Zhi H, Li R, Wang T,
Wang J, Wang L, Li X (2014) SNP@lincTFBS: an
integrated database of polymorphisms in human
LincRNA transcription factor binding sites. PLoS
One 9(7):e103851
52. Harrow J, Frankish A, Gonzalez JM, Tapanari E,
Diekhans M, Kokocinski F, Aken BL, Barrell D,
Zadissa A, Searle S et al (2012) GENCODE: the
reference human genome annotation for the ENCODE
project. Genome Res 22(9):1760–1774
53. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar
BT, Lowe CB, Wenger AM, Bejerano G (2010)
GREAT improves functional interpretation of
cis-regulatory regions. Nat Biotechnol 28(5):495–501
54. Karolchik D, Kuhn RM, Baertsch R, Barber GP,
Clawson H, Diekhans M, Giardine B, Harte RA,
Hinrichs AS, Hsu F et al (2008) The UCSC genome
browser database: 2008 update. Nucleic Acids Res 36
(Database issue):D773–D779