Variant report

Variant	rs3770112
Chromosome Location	chr2:182377541-182377542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10203974	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204136	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037624	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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490687	0.90[ASN][1000 genomes]
rs1143676	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11675041	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11675121	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11675166	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11680383	0.90[ASN][1000 genomes]
rs11686132	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11686167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11687348	0.86[ASN][1000 genomes]
rs11689738	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12469449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13032116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1349197	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375488	0.90[ASN][1000 genomes]
rs1375490	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1551033	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17225354	0.85[CEU][hapmap]
rs17226637	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17304246	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17304344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1823336	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1839266	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1964511	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964512	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124442	0.91[ASN][1000 genomes]
rs2305583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2305584	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2368212	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2887192	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770104	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770105	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770107	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770110	1.00[ASW][hapmap];1.00[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];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770115	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3816521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41265949	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4368293	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4667316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56095368	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56136548	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62189983	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62191451	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62191453	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6433921	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6433922	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6728886	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6747500	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6757312	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs767500	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs921257	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1002647	chr2:182078521-182392273	Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv536064	chr2:182078521-182392273	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1014910	chr2:182375267-182544114	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv536065	chr2:182375267-182544114	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3770112	CWC22	cis	cerebellum	SCAN
rs3770112	ITGA4	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182324400-182410400	Weak transcription	NHLF	lung
2	chr2:182330000-182390200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:182331400-182382200	Weak transcription	HMEC	breast
4	chr2:182334600-182381400	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:182335000-182405800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr2:182336800-182382800	Weak transcription	Small Intestine	intestine
7	chr2:182338200-182378400	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr2:182338200-182383400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr2:182338200-182399400	Weak transcription	Colonic Mucosa	Colon
10	chr2:182338200-182406800	Strong transcription	Fetal Thymus	thymus
11	chr2:182338200-182406800	Weak transcription	Spleen	Spleen
12	chr2:182338400-182382200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:182338600-182405600	Strong transcription	Primary B cells from peripheral blood	blood
14	chr2:182339000-182381000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:182339200-182380600	Strong transcription	Dnd41	blood
16	chr2:182339400-182405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:182346000-182378600	Weak transcription	Lung	lung
18	chr2:182347200-182399800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:182349600-182405800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:182350400-182384600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:182353800-182404200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:182355200-182383000	Strong transcription	GM12878-XiMat	blood
23	chr2:182356000-182406800	Strong transcription	Primary B cells from cord blood	blood
24	chr2:182356200-182379600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:182357000-182377800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:182358200-182405800	Strong transcription	Primary hematopoietic stem cells	blood
27	chr2:182359600-182391800	Weak transcription	Adipose Nuclei	Adipose
28	chr2:182361800-182398000	Weak transcription	Fetal Intestine Small	intestine
29	chr2:182362400-182380400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:182364000-182399200	Weak transcription	HSMM	muscle
31	chr2:182366200-182390200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:182366400-182399600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:182366600-182377600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr2:182367200-182377800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:182371600-182379600	Strong transcription	Primary T cells from cord blood	blood
36	chr2:182373200-182381200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:182373800-182379800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:182374200-182378600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:182374200-182379400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:182374200-182381400	Strong transcription	HSMMtube	muscle
41	chr2:182374400-182380200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:182374800-182380000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:182375000-182379000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr2:182375000-182379800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:182375400-182381800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:182376200-182378800	Strong transcription	NHDF-Ad	bronchial
47	chr2:182376200-182379000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:182376400-182379600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:182376600-182377600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:182376600-182379000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links