Variant report

Variant	rs2120107
Chromosome Location	chr15:76869789-76869790
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 12 )

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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1116535	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1117367	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]
rs1125932	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12148452	0.82[ASN][1000 genomes]
rs12148786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12148805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12437627	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12438077	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12441247	0.85[ASN][1000 genomes]
rs12441433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12441550	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12443137	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592171	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12594212	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594541	0.96[AMR][1000 genomes];0.96[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	0.97[AMR][1000 genomes];0.99[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];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12907805	0.95[CHB][hapmap];0.87[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];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs12916573	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1471780	0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1587381	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs17364076	0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs17364330	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs17460201	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1838050	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1867197	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1874944	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1946650	0.90[ASN][1000 genomes]
rs2056544	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2083762	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2117369	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2120108	0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2304920	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2404602	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs2404736	0.91[ASN][1000 genomes]
rs2404737	0.91[ASN][1000 genomes]
rs2404740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404741	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2454454	0.91[MEX][hapmap]
rs2461870	0.91[MEX][hapmap]
rs284895	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs2896954	0.91[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];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4641709	0.95[CHB][hapmap];0.87[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];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4886801	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs4886805	0.82[GIH][hapmap]
rs4886813	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4886817	0.89[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4886818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886824	0.81[ASN][1000 genomes]
rs4886825	0.95[CHB][hapmap];0.84[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7167613	0.82[ASN][1000 genomes]
rs7174953	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7179142	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs7181506	0.80[GIH][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];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8024476	0.82[ASN][1000 genomes]
rs8030411	0.94[CHB][hapmap];0.87[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:22 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2120107	SCAPER	cis	lung	GTEx
rs2120107	SCAPER	cis	Artery Tibial	GTEx
rs2120107	SCAPER	cis	Nerve Tibial	GTEx
rs2120107	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs2120107	SCAPER	cis	parietal	SCAN
rs2120107	SCAPER	cis	Thyroid	GTEx
rs2120107	TBC1D2B	cis	parietal	SCAN
rs2120107	SCAPER	cis	Esophagus Mucosa	GTEx
rs2120107	SCAPER	cis	cerebellum	SCAN
rs2120107	NRG4	cis	parietal	SCAN
rs2120107	GRAMD2	cis	cerebellum	SCAN
rs2120107	ZNF291	cis	multi-tissue	Pritchard

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76862600-76872000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr15:76868200-76870000	Weak transcription	Primary B cells from cord blood	blood
3	chr15:76868400-76869800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:76868400-76870800	Enhancers	Esophagus	oesophagus
5	chr15:76868400-76871000	Enhancers	Ovary	ovary
6	chr15:76868600-76870800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr15:76868800-76869800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:76868800-76869800	Enhancers	Adipose Nuclei	Adipose
9	chr15:76868800-76869800	Enhancers	Fetal Intestine Small	intestine
10	chr15:76868800-76869800	Flanking Active TSS	Hela-S3	cervix
11	chr15:76868800-76870000	Enhancers	Liver	Liver
12	chr15:76868800-76870200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr15:76868800-76870200	Enhancers	Small Intestine	intestine
14	chr15:76868800-76870600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr15:76868800-76870800	Enhancers	Right Atrium	heart
16	chr15:76868800-76871000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr15:76868800-76871200	Enhancers	NHEK	skin
18	chr15:76869000-76869800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:76869000-76869800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:76869000-76869800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr15:76869000-76869800	Enhancers	Pancreas	Pancrea
22	chr15:76869000-76869800	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr15:76869000-76869800	Enhancers	NHDF-Ad	bronchial
24	chr15:76869000-76870000	Enhancers	Colon Smooth Muscle	Colon
25	chr15:76869000-76870000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr15:76869000-76870000	Enhancers	Fetal Intestine Large	intestine
27	chr15:76869000-76870000	Enhancers	Psoas Muscle	Psoas
28	chr15:76869000-76870200	Enhancers	Brain Substantia Nigra	brain
29	chr15:76869000-76870200	Enhancers	Fetal Lung	lung
30	chr15:76869000-76870200	Enhancers	Fetal Muscle Leg	muscle
31	chr15:76869000-76870200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr15:76869000-76870400	Enhancers	Right Ventricle	heart
33	chr15:76869000-76870800	Enhancers	Aorta	Aorta
34	chr15:76869000-76870800	Enhancers	Left Ventricle	heart
35	chr15:76869000-76870800	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr15:76869000-76870800	Enhancers	HepG2	liver
37	chr15:76869000-76870800	Enhancers	HMEC	breast
38	chr15:76869000-76871000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:76869200-76869800	Enhancers	Fetal Muscle Trunk	muscle
40	chr15:76869200-76869800	Enhancers	Stomach Mucosa	stomach
41	chr15:76869200-76869800	Enhancers	Spleen	Spleen
42	chr15:76869200-76869800	Enhancers	HSMMtube	muscle
43	chr15:76869200-76870000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:76869200-76870000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr15:76869200-76870400	Enhancers	Lung	lung
46	chr15:76869400-76870000	Enhancers	Brain Cingulate Gyrus	brain
47	chr15:76869400-76870200	Enhancers	Fetal Heart	heart
48	chr15:76869400-76870600	Weak transcription	Fetal Thymus	thymus
49	chr15:76869400-76881200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:76869600-76870200	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links