Variant report

Variant	rs4957341
Chromosome Location	chr5:40678049-40678050
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	chr5:40677912-40680908	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:40678044-40678518	HUVEC	blood vessel:	n/a	n/a
3	NFYB	chr5:40677960-40678456	GM12878	blood:	n/a	n/a
4	MYC	chr5:40677879-40679478	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr5:40677884-40680287	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr5:40677211-40679447	MCF10A-Er-Src	breast:	n/a	chr5:40678336-40678347 chr5:40678826-40678840 chr5:40678828-40678837 chr5:40678827-40678838 chr5:40679028-40679042 chr5:40678829-40678838 chr5:40677774-40677782 chr5:40678832-40678840 chr5:40678844-40678852
7	POLR2A	chr5:40678049-40678626	HUVEC	blood vessel:	n/a	n/a
8	STAT3	chr5:40677902-40679305	MCF10A-Er-Src	breast:	n/a	chr5:40678336-40678347 chr5:40678826-40678840 chr5:40678828-40678837 chr5:40678827-40678838 chr5:40679028-40679042 chr5:40678829-40678838 chr5:40678832-40678840 chr5:40678844-40678852
9	STAT3	chr5:40677717-40679441	MCF10A-Er-Src	breast:	n/a	chr5:40678336-40678347 chr5:40678826-40678840 chr5:40678828-40678837 chr5:40678827-40678838 chr5:40679028-40679042 chr5:40678829-40678838 chr5:40677774-40677782 chr5:40678832-40678840 chr5:40678844-40678852

No.	Distal block	Cell Line	Cell type
1	chr5:40673402..40675876-chr5:40676322..40679263,4	K562	blood:
2	chr5:40505949..40508818-chr5:40677222..40679235,2	MCF-7	breast:
3	chr5:40677072..40679518-chr5:40680792..40683406,4	MCF-7	breast:

Variant related genes	Relation type
PTGER4	TF binding region
ENSG00000171522	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1395085	0.81[AFR][1000 genomes]
rs16870224	0.94[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs16870378	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs3792822	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs3805486	0.94[CHB][hapmap];0.90[CHD][hapmap]
rs4432939	0.96[ASN][1000 genomes]
rs6451534	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6861121	0.97[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880993	chr5:40521648-40682550	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	38 gene(s)	inside rSNPs	diseases
2	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40668800-40678600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:40672000-40678400	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr5:40672600-40678600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:40672800-40678600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr5:40673400-40678600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr5:40673400-40678600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr5:40674600-40678200	Enhancers	HMEC	breast
8	chr5:40674600-40678600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:40674800-40678400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr5:40674800-40678400	Enhancers	Fetal Thymus	thymus
11	chr5:40675200-40678800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr5:40675600-40678200	Enhancers	Thymus	Thymus
13	chr5:40675800-40678400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr5:40675800-40679000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:40676000-40678200	Enhancers	Fetal Intestine Small	intestine
16	chr5:40676000-40678800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr5:40676000-40679000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:40676000-40679000	Weak transcription	Esophagus	oesophagus
19	chr5:40676200-40678200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:40676200-40678600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr5:40676400-40678800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr5:40676600-40678600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:40676800-40678200	Flanking Active TSS	Dnd41	blood
24	chr5:40676800-40678200	Enhancers	NHDF-Ad	bronchial
25	chr5:40676800-40678400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr5:40676800-40678600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:40676800-40679200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:40676800-40679200	Flanking Active TSS	HUVEC	blood vessel
29	chr5:40677000-40678400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr5:40677000-40679000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:40677000-40679000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr5:40677200-40678200	Weak transcription	NHLF	lung
33	chr5:40677200-40678600	Flanking Active TSS	NHEK	skin
34	chr5:40677400-40678200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:40677400-40678200	Enhancers	Hela-S3	cervix
36	chr5:40677400-40678200	Enhancers	HSMM	muscle
37	chr5:40677400-40678400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr5:40677400-40678400	Enhancers	HSMMtube	muscle
39	chr5:40677400-40678600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr5:40677400-40678600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:40677400-40678600	Weak transcription	Colonic Mucosa	Colon
42	chr5:40677400-40678600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:40677400-40678800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:40677400-40678800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:40677400-40679000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr5:40677400-40679000	Weak transcription	Gastric	stomach
47	chr5:40677400-40679000	Weak transcription	Pancreas	Pancrea
48	chr5:40677400-40679000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:40677400-40679000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr5:40677400-40680800	Active TSS	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links