Variant report

Variant	rs6890006
Chromosome Location	chr5:40677218-40677219
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	chr5:40677031-40677670	HUVEC	blood vessel:	n/a	n/a
2	JUND	chr5:40677141-40677478	H1-hESC	embryonic stem cell:	n/a	chr5:40677335-40677346 chr5:40677334-40677342 chr5:40677332-40677344
3	RAD21	chr5:40677118-40677516	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr5:40676696-40677471	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr5:40676695-40677502	H1-neurons	neurons:	n/a	n/a
6	FOS	chr5:40677080-40677580	HUVEC	blood vessel:	n/a	chr5:40677335-40677346 chr5:40677334-40677342 chr5:40677332-40677344 chr5:40677332-40677343
7	POLR2A	chr5:40677096-40677821	HUVEC	blood vessel:	n/a	n/a
8	MAX	chr5:40676869-40677474	Hela-S3	cervix:	n/a	chr5:40677334-40677343
9	FOS	chr5:40677163-40677541	MCF10A-Er-Src	breast:	n/a	chr5:40677335-40677346 chr5:40677334-40677342 chr5:40677332-40677344 chr5:40677332-40677343
10	CTCF	chr5:40677180-40677330	AG04450	lung:	n/a	n/a
11	REST	chr5:40676722-40677496	H1-neurons	neurons:	n/a	chr5:40676976-40676986
12	FOS	chr5:40676942-40677494	MCF10A-Er-Src	breast:	n/a	chr5:40677335-40677346 chr5:40677334-40677342 chr5:40677332-40677344 chr5:40677332-40677343
13	MYC	chr5:40676805-40677246	NB4	blood:	n/a	n/a
14	JUN	chr5:40677149-40677533	HUVEC	blood vessel:	n/a	chr5:40677335-40677346 chr5:40677334-40677342 chr5:40677332-40677344
15	FOS	chr5:40677162-40677490	MCF10A-Er-Src	breast:	n/a	chr5:40677335-40677346 chr5:40677334-40677342 chr5:40677332-40677344 chr5:40677332-40677343
16	REST	chr5:40676423-40677666	H1-neurons	neurons:	n/a	chr5:40676976-40676986
17	TCF12	chr5:40677150-40677523	H1-hESC	embryonic stem cell:	n/a	chr5:40677503-40677512 chr5:40677299-40677306
18	STAT3	chr5:40677197-40677528	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr5:40676866-40677598	MCF10A-Er-Src	breast:	n/a	n/a
20	MYC	chr5:40676843-40677419	MCF10A-Er-Src	breast:	n/a	chr5:40677334-40677343
21	GATA2	chr5:40677152-40677551	HUVEC	blood vessel:	n/a	n/a
22	MAX	chr5:40676817-40677273	NB4	blood:	n/a	n/a
23	POLR2A	chr5:40677169-40677859	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr5:40677035-40677454	HUVEC	blood vessel:	n/a	n/a
25	FOS	chr5:40677180-40677481	MCF10A-Er-Src	breast:	n/a	chr5:40677335-40677346 chr5:40677334-40677342 chr5:40677332-40677344 chr5:40677332-40677343
26	CTCF	chr5:40677140-40677290	HEK293	kidney:	n/a	n/a
27	USF2	chr5:40677139-40677285	Hela-S3	cervix:	n/a	n/a
28	RAD21	chr5:40677121-40677557	IMR90	lung:	n/a	n/a
29	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
30	STAT3	chr5:40677182-40677516	MCF10A-Er-Src	breast:	n/a	n/a
31	STAT3	chr5:40676931-40677401	MCF10A-Er-Src	breast:	n/a	n/a
32	TCF7L2	chr5:40677153-40677545	Hela-S3	cervix:	n/a	chr5:40677424-40677433 chr5:40677421-40677437 chr5:40677422-40677436 chr5:40677421-40677437
33	SMC3	chr5:40677166-40677732	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:40673402..40675876-chr5:40676322..40679263,4	K562	blood:
2	chr5:40677072..40679518-chr5:40680792..40683406,4	MCF-7	breast:
3	chr5:40676137..40677874-chr5:40679595..40681431,2	K562	blood:

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

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs58997800	1.00[AMR][1000 genomes]
rs59321002	1.00[AMR][1000 genomes]
rs9687153	1.00[AMR][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:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40668600-40677600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr5:40668800-40678600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr5:40672000-40678400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr5:40672600-40678600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr5:40672800-40678600	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr5:40673400-40678600	Weak transcription	Primary B cells from peripheral blood	blood
7	chr5:40673400-40678600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr5:40674600-40678200	Enhancers	HMEC	breast
9	chr5:40674600-40678600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:40674800-40677400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr5:40674800-40678400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:40674800-40678400	Enhancers	Fetal Thymus	thymus
13	chr5:40675000-40677400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:40675000-40677600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr5:40675200-40678800	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr5:40675600-40678200	Enhancers	Thymus	Thymus
17	chr5:40675800-40677400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:40675800-40678400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr5:40675800-40679000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:40676000-40678200	Enhancers	Fetal Intestine Small	intestine
21	chr5:40676000-40678800	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr5:40676000-40679000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:40676000-40679000	Weak transcription	Esophagus	oesophagus
24	chr5:40676200-40677800	Enhancers	Primary hematopoietic stem cells	blood
25	chr5:40676200-40678200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:40676200-40678600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr5:40676400-40678800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:40676600-40677400	Enhancers	Gastric	stomach
29	chr5:40676600-40677600	Enhancers	Adipose Nuclei	Adipose
30	chr5:40676600-40677600	Enhancers	Fetal Muscle Leg	muscle
31	chr5:40676600-40678600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:40676800-40677400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:40676800-40677400	Enhancers	Colon Smooth Muscle	Colon
34	chr5:40676800-40677400	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr5:40676800-40677400	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr5:40676800-40677400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr5:40676800-40677400	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr5:40676800-40677400	Flanking Active TSS	Hela-S3	cervix
39	chr5:40676800-40677400	Flanking Active TSS	HSMM	muscle
40	chr5:40676800-40677600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr5:40676800-40677600	Enhancers	H1 Cell Line	embryonic stem cell
42	chr5:40676800-40677600	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr5:40676800-40677600	Enhancers	NH-A	brain
44	chr5:40676800-40677800	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr5:40676800-40677800	Enhancers	Stomach Mucosa	stomach
46	chr5:40676800-40678000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr5:40676800-40678000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr5:40676800-40678000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr5:40676800-40678200	Flanking Active TSS	Dnd41	blood
50	chr5:40676800-40678200	Enhancers	NHDF-Ad	bronchial

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