Variant report

Variant	rs12915366
Chromosome Location	chr15:78831753-78831754
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:78831361-78831838	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr15:78830840-78834174	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:78831151-78834112	GM12878	blood:	n/a	n/a
4	MAFF	chr15:78831556-78831794	K562	blood:	n/a	n/a
5	POLR2A	chr15:78830693-78835554	GM12891	blood:	n/a	n/a
6	MAFK	chr15:78831679-78831758	Hela-S3	cervix:	n/a	chr15:78831741-78831752 chr15:78831740-78831751 chr15:78831740-78831751
7	POLR2A	chr15:78831504-78834721	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr15:78831753-78833808	GM12892	blood:	n/a	n/a
9	POLR2A	chr15:78831558-78831753	HepG2	liver:	n/a	n/a
10	MAFF	chr15:78831598-78831857	HepG2	liver:	n/a	n/a
11	HCFC1	chr15:78831559-78834951	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr15:78831547-78834072	GM12878	blood:	n/a	n/a
13	MAFK	chr15:78831605-78831832	HepG2	liver:	n/a	chr15:78831741-78831752 chr15:78831740-78831751 chr15:78831740-78831751
14	IRF1	chr15:78831696-78831781	K562	blood:	n/a	n/a
15	POLR2A	chr15:78831674-78831874	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78831297..78836398-chr15:78856605..78860226,12	MCF-7	breast:
2	chr15:78797464..78804546-chr15:78829529..78835433,12	MCF-7	breast:
3	chr15:78829726..78832334-chr15:78857099..78858875,2	K562	blood:
4	chr15:78798809..78800718-chr15:78830322..78833228,2	K562	blood:
5	chr15:78831312..78834277-chr15:78872379..78875019,2	MCF-7	breast:
6	chr15:78798844..78801827-chr15:78830907..78834394,5	MCF-7	breast:
7	chr15:78803621..78806940-chr15:78831151..78833237,3	K562	blood:
8	chr15:78798048..78801609-chr15:78828919..78833228,5	K562	blood:
9	chr15:78829726..78834442-chr15:78855710..78860360,8	K562	blood:

Variant related genes	Relation type
PSMA4	TF binding region
ENSG00000188266	Chromatin interaction
ENSG00000169684	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11630349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632604	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636131	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858230	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12591557	0.91[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594391	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12900612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12900783	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12902493	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12903129	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12906284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906846	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12906951	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12907966	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910100	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910289	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910726	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910969	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910978	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12912022	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12912673	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12913173	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12914694	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12916483	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916999	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504545	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1504546	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504548	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17407257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847530	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979905	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979906	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979907	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979908	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292117	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28392948	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28438420	0.91[EUR][1000 genomes]
rs2869055	0.91[EUR][1000 genomes]
rs2869544	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3743077	0.81[TSI][hapmap]
rs3813571	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813572	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243083	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886571	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886572	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4887062	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4887063	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4887064	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5022780	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55690619	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56007453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008174	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62008193	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62008194	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7164030	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8025429	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8053	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs880395	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs905740	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs952215	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs952216	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs12915366	CHRNA5	cis	Nerve Tibial	GTEx
rs12915366	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs12915366	CHRNA5	cis	cerebellum	SCAN
rs12915366	IREB2	cis	cerebellum	SCAN
rs12915366	CHRNA5	cis	parietal	SCAN
rs12915366	CHRNA5	cis	Heart Left Ventricle	GTEx
rs12915366	PSMA4	cis	cerebellum	SCAN
rs12915366	CHRNA3	cis	Muscle Skeletal	GTEx
rs12915366	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs12915366	CHRNA5	cis	Esophagus Mucosa	GTEx
rs12915366	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs12915366	IREB2	cis	parietal	SCAN
rs12915366	CHRNA5	cis	lung	GTEx
rs12915366	CHRNA5	cis	Muscle Skeletal	GTEx
rs12915366	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs12915366	RP11-650L12.2	cis	lung	GTEx
rs12915366	UBE2Q2	cis	cerebellum	SCAN
rs12915366	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78800800-78832000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr15:78800800-78832200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:78800800-78832200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:78800800-78832400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:78801000-78832200	Weak transcription	Adipose Nuclei	Adipose
6	chr15:78801000-78832200	Weak transcription	Fetal Kidney	kidney
7	chr15:78801000-78832200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:78801000-78832200	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:78801000-78832200	Weak transcription	A549	lung
10	chr15:78803000-78832200	Weak transcription	Primary T cells from cord blood	blood
11	chr15:78810600-78832000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:78810600-78832400	Weak transcription	Aorta	Aorta
13	chr15:78810800-78832200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:78812000-78832200	Weak transcription	Fetal Stomach	stomach
15	chr15:78812400-78832200	Weak transcription	Fetal Intestine Large	intestine
16	chr15:78812600-78832200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr15:78816600-78832200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:78817000-78832200	Weak transcription	Fetal Intestine Small	intestine
19	chr15:78821200-78832200	Weak transcription	Left Ventricle	heart
20	chr15:78821200-78832400	Weak transcription	Ovary	ovary
21	chr15:78821400-78832200	Weak transcription	Liver	Liver
22	chr15:78826000-78832200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:78826000-78832200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:78826200-78832200	Weak transcription	Brain Anterior Caudate	brain
25	chr15:78826200-78832200	Weak transcription	Brain Hippocampus Middle	brain
26	chr15:78828800-78832400	Enhancers	Fetal Heart	heart
27	chr15:78829400-78832200	Weak transcription	GM12878-XiMat	blood
28	chr15:78830400-78832000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:78830800-78832000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr15:78830800-78832200	Weak transcription	Fetal Muscle Leg	muscle
31	chr15:78831400-78832200	Weak transcription	Right Ventricle	heart
32	chr15:78831400-78832200	Weak transcription	K562	blood
33	chr15:78831600-78832200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links