Variant report

Variant	rs7602504
Chromosome Location	chr2:182387133-182387134
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	chr2:182387083-182387671	HL-60	blood:	n/a	n/a
2	POLR2A	chr2:182386888-182387694	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:182377600..182382674-chr2:182385236..182387590,5	MCF-7	breast:

Variant related genes	Relation type
ITGA4	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10203974	1.00[LWK][hapmap];0.91[YRI][hapmap]
rs10204136	1.00[LWK][hapmap];0.91[YRI][hapmap]
rs1026403	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10490692	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1143674	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11886182	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11890431	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12478032	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12690516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12997453	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13003064	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13034078	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1349197	1.00[LWK][hapmap];0.83[YRI][hapmap]
rs1375491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1551031	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17226490	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2887191	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3770108	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667309	1.00[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4667316	0.93[LWK][hapmap];0.83[YRI][hapmap]
rs6707704	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6714061	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6721763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6748657	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7562325	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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

No data

Chromatin state (count:60 , 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	chr2:182335000-182405800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr2:182338200-182399400	Weak transcription	Colonic Mucosa	Colon
5	chr2:182338200-182406800	Strong transcription	Fetal Thymus	thymus
6	chr2:182338200-182406800	Weak transcription	Spleen	Spleen
7	chr2:182338600-182405600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr2:182339400-182405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:182347200-182399800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:182349600-182405800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:182353800-182404200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:182356000-182406800	Strong transcription	Primary B cells from cord blood	blood
13	chr2:182358200-182405800	Strong transcription	Primary hematopoietic stem cells	blood
14	chr2:182359600-182391800	Weak transcription	Adipose Nuclei	Adipose
15	chr2:182361800-182398000	Weak transcription	Fetal Intestine Small	intestine
16	chr2:182364000-182399200	Weak transcription	HSMM	muscle
17	chr2:182366200-182390200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:182366400-182399600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:182377200-182396800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:182378200-182390800	Weak transcription	NH-A	brain
21	chr2:182378800-182387600	Weak transcription	NHDF-Ad	bronchial
22	chr2:182378800-182389800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:182380200-182390000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:182380600-182390400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:182381200-182397800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr2:182381600-182389400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr2:182382600-182405600	Strong transcription	Dnd41	blood
28	chr2:182382800-182406200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:182383000-182387400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:182383000-182390000	Weak transcription	Left Ventricle	heart
31	chr2:182383000-182404600	Weak transcription	Esophagus	oesophagus
32	chr2:182383000-182405800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr2:182383000-182406000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:182383400-182387200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:182383400-182388200	Weak transcription	HMEC	breast
36	chr2:182383400-182404600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:182383600-182405600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr2:182383600-182405600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:182384200-182389200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr2:182384200-182406000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:182384200-182406400	Strong transcription	Primary T cells from cord blood	blood
42	chr2:182384600-182388800	Strong transcription	Thymus	Thymus
43	chr2:182384600-182397200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr2:182385000-182388200	Weak transcription	NHEK	skin
45	chr2:182385000-182388400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:182385200-182388200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:182385200-182389800	Weak transcription	Aorta	Aorta
48	chr2:182385200-182390200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr2:182385400-182388000	Weak transcription	HSMMtube	muscle
50	chr2:182385600-182389800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links