Variant report

Variant	rs1494562
Chromosome Location	chr5:35854265-35854266
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	BHLHE40	chr5:35854183-35854767	GM12878	blood:	n/a	n/a
2	PAX5	chr5:35854186-35854377	GM12878	blood:	n/a	chr5:35854211-35854220

Variant related genes	Relation type
IL7R	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10044838	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10044883	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10058453	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10063445	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10074095	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10074127	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10941267	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11567686	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11567737	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1353250	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1353252	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1389830	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1389831	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1389832	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1494555	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1494556	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1494557	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1494558	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1494560	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1494561	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1862634	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3777090	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6451226	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6451227	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6451228	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6451230	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6451231	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6893142	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7701111	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7711202	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7711208	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7711268	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7716064	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7720993	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292616	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9292617	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs969129	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][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	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv881055	chr5:35850693-35858721	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv881685	chr5:35850693-35859863	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv881358	chr5:35850693-35861068	Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv880610	chr5:35850693-35866265	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv880517	chr5:35850693-35870814	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35849600-35856200	Enhancers	Dnd41	blood
2	chr5:35851800-35856800	Enhancers	NHDF-Ad	bronchial
3	chr5:35852000-35854400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:35852000-35854600	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr5:35852000-35856800	Enhancers	Primary B cells from cord blood	blood
6	chr5:35852200-35854400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr5:35852200-35854400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:35852200-35854600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
9	chr5:35852400-35854400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr5:35852400-35856200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:35852400-35856600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:35852400-35859200	Weak transcription	Lung	lung
13	chr5:35852400-35862800	Enhancers	Hela-S3	cervix
14	chr5:35852600-35855600	Weak transcription	A549	lung
15	chr5:35852600-35856400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:35852800-35854400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr5:35852800-35854400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr5:35852800-35854400	Weak transcription	HMEC	breast
19	chr5:35852800-35854800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:35852800-35856000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:35852800-35856600	Weak transcription	NH-A	brain
22	chr5:35852800-35857000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr5:35853000-35855400	Weak transcription	HSMMtube	muscle
24	chr5:35853000-35855400	Weak transcription	NHLF	lung
25	chr5:35853000-35856400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:35853000-35856400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:35853000-35856600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:35853000-35856600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:35853000-35856800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr5:35853000-35857000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:35853200-35854400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:35853400-35855200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:35853400-35855400	Weak transcription	HSMM	muscle
34	chr5:35853600-35854600	Flanking Active TSS	Thymus	Thymus
35	chr5:35853600-35854800	Weak transcription	Osteobl	bone
36	chr5:35853600-35856800	Enhancers	Fetal Thymus	thymus
37	chr5:35853800-35854400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:35853800-35854600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
39	chr5:35853800-35855200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:35853800-35855400	Enhancers	Primary B cells from peripheral blood	blood
41	chr5:35853800-35856400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr5:35853800-35857200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr5:35853800-35858000	Enhancers	GM12878-XiMat	blood
44	chr5:35854000-35854400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:35854000-35854400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr5:35854000-35854400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:35854000-35854400	Active TSS	Right Atrium	heart
48	chr5:35854000-35855600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr5:35854200-35854400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr5:35854200-35856400	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links