Variant report

Variant	rs1117367
Chromosome Location	chr15:76872330-76872331
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10444858	0.82[ASN][1000 genomes]
rs11072599	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11072603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1116535	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1125932	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12148452	0.82[ASN][1000 genomes]
rs12148786	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148805	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12437627	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12438077	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12441247	0.85[ASN][1000 genomes]
rs12441433	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441550	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12443137	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592171	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12594212	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594541	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594577	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12595313	0.82[ASN][1000 genomes]
rs12898430	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899871	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12900494	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12902174	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12907805	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs12908421	0.89[ASN][1000 genomes]
rs12911987	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs12915248	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs12916573	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1471780	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1587381	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs17364076	0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs17364330	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs17460201	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1838050	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1867197	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1874944	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1946650	0.90[ASN][1000 genomes]
rs2056544	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2083762	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2117369	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2120107	1.00[ASW][hapmap];0.96[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];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120108	0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2304920	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2404602	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs2404736	0.91[ASN][1000 genomes]
rs2404737	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2404740	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404741	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454454	0.91[MEX][hapmap]
rs2461870	0.91[MEX][hapmap]
rs284895	0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs2896954	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34060246	0.82[ASN][1000 genomes]
rs34707035	0.82[ASN][1000 genomes]
rs34924128	0.82[ASN][1000 genomes]
rs35138393	0.82[ASN][1000 genomes]
rs35395069	0.82[ASN][1000 genomes]
rs35498563	0.82[ASN][1000 genomes]
rs35566346	0.87[ASN][1000 genomes]
rs3816266	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4079681	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs437131	0.82[GIH][hapmap]
rs4383105	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4442773	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4633676	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4641709	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4886496	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4886799	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4886801	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4886805	0.82[GIH][hapmap]
rs4886813	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4886817	0.89[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4886818	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886824	0.81[ASN][1000 genomes]
rs4886825	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs55676827	0.82[ASN][1000 genomes]
rs56351018	0.85[ASN][1000 genomes]
rs58361452	0.82[ASN][1000 genomes]
rs58511211	0.85[ASN][1000 genomes]
rs58973160	0.82[ASN][1000 genomes]
rs59088060	0.90[ASN][1000 genomes]
rs60912217	0.80[ASN][1000 genomes]
rs6495206	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66754747	0.85[ASN][1000 genomes]
rs67010831	0.82[ASN][1000 genomes]
rs67204011	0.90[ASN][1000 genomes]
rs67570291	0.82[ASN][1000 genomes]
rs71405216	0.87[ASN][1000 genomes]
rs71405223	0.82[ASN][1000 genomes]
rs7163946	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7164060	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7164813	0.95[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs7167613	0.82[ASN][1000 genomes]
rs7174673	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7174953	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7179142	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs72738889	0.82[ASN][1000 genomes]
rs7342603	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7350777	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8024476	0.82[ASN][1000 genomes]
rs8030411	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs8036703	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs8039545	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8040539	0.85[JPT][hapmap]
rs8043474	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9646213	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542438	chr15:76697056-76892157	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
2	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1042514	chr15:76838221-76906382	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
12	nsv1038233	chr15:76855205-76895763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1037282	chr15:76859309-76895763	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1044453	chr15:76860198-76895763	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
15	nsv1620	chr15:76862152-76914288	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
16	nsv904402	chr15:76863023-76930805	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
17	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
18	nsv1042623	chr15:76863437-76999030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1039269	chr15:76863437-77057021	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
20	nsv1048577	chr15:76868215-76895763	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
21	nsv1051037	chr15:76868215-76902257	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
22	nsv1038521	chr15:76869789-76895763	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
23	nsv1042304	chr15:76869929-76895763	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
24	esv3584695	chr15:76869929-76895775	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
25	nsv1042883	chr15:76869929-76902458	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
26	nsv904403	chr15:76869929-76951040	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
27	nsv904404	chr15:76869929-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
28	nsv904405	chr15:76869929-77047915	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
29	nsv904406	chr15:76869929-77085283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
30	nsv904407	chr15:76869929-77121196	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1117367	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs1117367	SCAPER	cis	Nerve Tibial	GTEx
rs1117367	SCAPER	cis	lung	GTEx
rs1117367	SCAPER	cis	Thyroid	GTEx
rs1117367	SCAPER	cis	Artery Tibial	GTEx
rs1117367	SCAPER	cis	Esophagus Mucosa	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76869400-76881200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:76870200-76872600	Weak transcription	Brain Substantia Nigra	brain
3	chr15:76870400-76876000	Weak transcription	Right Ventricle	heart
4	chr15:76870400-76881200	Weak transcription	Lung	lung
5	chr15:76870800-76874000	Weak transcription	Esophagus	oesophagus
6	chr15:76871000-76883600	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links