Variant report

Variant	rs6861640
Chromosome Location	chr5:37669246-37669247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:37659630..37663695-chr5:37665450..37669812,5	K562	blood:
2	chr5:37619614..37621754-chr5:37668153..37669761,2	MCF-7	breast:
3	chr5:37667989..37670619-chr5:37702239..37705026,2	MCF-7	breast:
4	chr5:37662824..37665076-chr5:37668148..37670201,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222743	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10050392	1.00[CEU][hapmap]
rs10053094	1.00[CEU][hapmap]
rs10055123	1.00[CEU][hapmap]
rs10058062	1.00[CEU][hapmap]
rs10059214	1.00[CEU][hapmap]
rs10063001	1.00[CEU][hapmap]
rs10071967	1.00[CEU][hapmap]
rs10072326	1.00[CEU][hapmap]
rs10075851	1.00[CEU][hapmap]
rs1104717	1.00[CEU][hapmap]
rs1104718	1.00[CEU][hapmap]
rs11742290	1.00[CEU][hapmap]
rs12186464	1.00[CEU][hapmap]
rs12332493	1.00[CEU][hapmap]
rs13175777	1.00[CEU][hapmap]
rs16903667	1.00[CEU][hapmap]
rs16903675	1.00[CEU][hapmap]
rs16903689	1.00[CEU][hapmap]
rs16903703	1.00[CEU][hapmap]
rs16903704	1.00[CEU][hapmap]
rs16903706	1.00[CEU][hapmap]
rs16903711	1.00[CEU][hapmap]
rs1829294	1.00[CEU][hapmap]
rs4074950	1.00[CEU][hapmap]
rs4334908	1.00[CEU][hapmap]
rs4370304	1.00[CEU][hapmap]
rs475517	1.00[CEU][hapmap]
rs587641	1.00[CEU][hapmap]
rs6863547	1.00[CEU][hapmap]
rs6868843	1.00[CEU][hapmap]
rs6869205	1.00[CEU][hapmap]
rs6888597	1.00[CEU][hapmap]
rs6898271	1.00[CEU][hapmap]
rs7703638	1.00[CEU][hapmap]
rs7703670	1.00[CEU][hapmap]
rs7704548	1.00[CEU][hapmap]
rs7708301	1.00[CEU][hapmap]
rs7708708	1.00[CEU][hapmap]
rs7710547	1.00[CEU][hapmap]
rs7714066	1.00[CEU][hapmap]
rs7724308	1.00[CEU][hapmap]
rs7725049	1.00[CEU][hapmap]
rs7727603	1.00[CEU][hapmap]
rs7729195	1.00[CEU][hapmap]
rs7736605	1.00[CEU][hapmap]
rs7736862	1.00[CEU][hapmap]
rs7737210	1.00[CEU][hapmap]
rs7737986	1.00[CEU][hapmap]
rs8180378	1.00[CEU][hapmap]
rs9292661	1.00[CEU][hapmap]
rs9292663	1.00[CEU][hapmap]
rs951579	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv432744	chr5:37374124-37743077	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv880890	chr5:37443079-37681646	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1030250	chr5:37478163-37734859	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37654600-37671800	Weak transcription	Primary T cells from cord blood	blood
2	chr5:37656600-37671600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:37662800-37671800	Weak transcription	Small Intestine	intestine
4	chr5:37664000-37671800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr5:37665400-37669400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:37665400-37669800	Enhancers	NHLF	lung
7	chr5:37665800-37671200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr5:37665800-37672400	Weak transcription	Primary B cells from cord blood	blood
9	chr5:37666200-37671800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:37666200-37672200	Weak transcription	Right Ventricle	heart
11	chr5:37666400-37669400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:37666400-37672400	Weak transcription	Left Ventricle	heart
13	chr5:37666600-37671800	Weak transcription	Fetal Heart	heart
14	chr5:37666800-37669600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:37666800-37671400	Weak transcription	Psoas Muscle	Psoas
16	chr5:37666800-37672400	Weak transcription	Adipose Nuclei	Adipose
17	chr5:37667000-37671000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:37667000-37672200	Weak transcription	Lung	lung
19	chr5:37667200-37669600	Weak transcription	Aorta	Aorta
20	chr5:37667400-37669400	Enhancers	Osteobl	bone
21	chr5:37667400-37669800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:37667400-37671800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:37667600-37669800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:37667600-37669800	Enhancers	HMEC	breast
25	chr5:37667600-37669800	Enhancers	NHDF-Ad	bronchial
26	chr5:37667800-37669800	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr5:37668000-37669400	Enhancers	HSMM	muscle
28	chr5:37668000-37669600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:37668000-37669800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr5:37668000-37669800	Enhancers	NH-A	brain
31	chr5:37668200-37669400	Enhancers	NHEK	skin
32	chr5:37668200-37670000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr5:37668800-37669400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:37668800-37671400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:37669000-37671800	Weak transcription	Ovary	ovary
36	chr5:37669200-37669400	Enhancers	Muscle Satellite Cultured Cells	--
37	chr5:37669200-37671000	Weak transcription	A549	lung
38	chr5:37669200-37671800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr5:37669200-37671800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:37669200-37671800	Weak transcription	K562	blood
41	chr5:37669200-37672400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:37669200-37672800	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links