Variant report

Variant	rs6977848
Chromosome Location	chr7:25989520-25989521
allele	G/T
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	CTCF	chr7:25989460-25989610	GM12864	blood:	n/a	chr7:25989478-25989487
2	ATF2	chr7:25989381-25989818	GM12878	blood:	n/a	n/a
3	SIN3A	chr7:25989265-25991735	H1-hESC	embryonic stem cell:	n/a	chr7:25990195-25990206 chr7:25990193-25990206 chr7:25991169-25991182 chr7:25990724-25990737 chr7:25991166-25991175 chr7:25991177-25991190 chr7:25990883-25990894
4	POLR2A	chr7:25985526-25991809	GM19099	blood:	n/a	n/a
5	HEY1	chr7:25989259-25989743	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:25989403-25989694	K562	blood:	n/a	n/a
7	WRNIP1	chr7:25989375-25989986	GM12878	blood:	n/a	n/a
8	MAX	chr7:25989415-25989589	HepG2	liver:	n/a	n/a
9	CTCF	chr7:25989420-25989570	GM12865	blood:	n/a	chr7:25989478-25989487
10	ZNF143	chr7:25989454-25990268	H1-hESC	embryonic stem cell:	n/a	chr7:25990014-25990024
11	MAX	chr7:25989212-25989717	HepG2	liver:	n/a	n/a
12	CTCF	chr7:25989440-25989590	GM12872	blood:	n/a	chr7:25989478-25989487
13	CTCF	chr7:25989400-25989550	HRE	kidney:	n/a	chr7:25989478-25989487
14	UBTF	chr7:25989383-25989586	K562	blood:	n/a	n/a
15	TBP	chr7:25989276-25989927	K562	blood:	n/a	n/a
16	MBD4	chr7:25989079-25989701	HepG2	liver:	n/a	n/a
17	CTCF	chr7:25989344-25989788	K562	blood:	n/a	chr7:25989478-25989487 chr7:25989645-25989653
18	POLR2A	chr7:25987021-25992694	HepG2	liver:	n/a	n/a
19	POLR2A	chr7:25986974-25991365	HepG2	liver:	n/a	n/a
20	CREB1	chr7:25989239-25991492	HepG2	liver:	n/a	n/a
21	MAX	chr7:25989331-25989883	GM12878	blood:	n/a	n/a
22	JUND	chr7:25989286-25989739	H1-hESC	embryonic stem cell:	n/a	n/a
23	REST	chr7:25989312-25989615	HepG2	liver:	n/a	n/a
24	POLR2A	chr7:25989248-25989702	HepG2	liver:	n/a	n/a
25	CTCF	chr7:25989426-25989558	H1-hESC	embryonic stem cell:	n/a	chr7:25989478-25989487
26	CTCF	chr7:25989344-25989770	K562	blood:	n/a	chr7:25989478-25989487 chr7:25989645-25989653
27	CTCF	chr7:25989460-25989610	GM12869	blood:	n/a	chr7:25989478-25989487
28	EBF1	chr7:25989348-25990122	GM12878	blood:	n/a	chr7:25989451-25989460 chr7:25989451-25989461 chr7:25989531-25989542
29	POLR2A	chr7:25989404-25990965	K562	blood:	n/a	n/a
30	CTCF	chr7:25989480-25989630	HMF	breast:	n/a	n/a
31	CTCF	chr7:25989440-25989590	Caco-2	colon:	n/a	chr7:25989478-25989487
32	MAZ	chr7:25989386-25989594	HepG2	liver:	n/a	n/a
33	POLR2A	chr7:25986274-25991748	GM18526	blood:	n/a	n/a
34	CTCF	chr7:25989440-25989590	GM12873	blood:	n/a	chr7:25989478-25989487
35	POLR2A	chr7:25989232-25989798	HepG2	liver:	n/a	n/a
36	POLR2A	chr7:25989121-25989633	K562	blood:	n/a	n/a
37	RAD21	chr7:25989398-25989642	H1-hESC	embryonic stem cell:	n/a	n/a
38	RAD21	chr7:25989382-25989753	HepG2	liver:	n/a	n/a
39	SP1	chr7:25989305-25989629	H1-hESC	embryonic stem cell:	n/a	chr7:25989444-25989458 chr7:25989443-25989455 chr7:25989445-25989454 chr7:25989444-25989454 chr7:25989443-25989455 chr7:25989444-25989453
40	CTCF	chr7:25989473-25989605	K562	blood:	n/a	chr7:25989478-25989487
41	CTCF	chr7:25989420-25989570	NHEK	skin:	n/a	chr7:25989478-25989487
42	MYC	chr7:25989428-25989635	K562	blood:	n/a	n/a
43	TAF1	chr7:25989308-25989735	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAX	chr7:25989202-25990609	H1-hESC	embryonic stem cell:	n/a	n/a
45	CTCF	chr7:25989420-25989570	GM12873	blood:	n/a	chr7:25989478-25989487
46	CTCF	chr7:25989480-25989630	GM12871	blood:	n/a	n/a
47	CTCF	chr7:25989480-25989630	GM12867	blood:	n/a	n/a
48	MAX	chr7:25989274-25989657	K562	blood:	n/a	n/a
49	CTCF	chr7:25989440-25989590	HEEpiC	esophagus:	n/a	chr7:25989478-25989487
50	CTCF	chr7:25989351-25989699	K562	blood:	n/a	chr7:25989478-25989487 chr7:25989645-25989653

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:25989265..25991851-chr7:26238825..26240746,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270933	TF binding region
ENSG00000122566	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10258485	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10951118	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10951119	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10951120	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10951121	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11760762	1.00[ASN][1000 genomes]
rs11983649	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12700679	1.00[ASN][1000 genomes]
rs12700680	1.00[ASN][1000 genomes]
rs12700681	1.00[ASN][1000 genomes]
rs12700682	1.00[ASN][1000 genomes]
rs13226851	1.00[ASN][1000 genomes]
rs13231897	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17729097	1.00[ASN][1000 genomes]
rs1966841	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2076881	1.00[JPT][hapmap]
rs2391172	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2391175	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2893222	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35336240	1.00[ASN][1000 genomes]
rs4000713	0.82[ASN][1000 genomes]
rs4236321	0.84[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412274	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4422683	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722543	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4722545	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722546	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722547	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722548	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4722550	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4722551	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs62446277	0.87[AFR][1000 genomes]
rs6461896	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66700050	1.00[ASN][1000 genomes]
rs66892818	0.86[AFR][1000 genomes]
rs67494041	1.00[ASN][1000 genomes]
rs6953596	0.87[AFR][1000 genomes]
rs6954557	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6963094	1.00[CHB][hapmap]
rs735316	1.00[ASN][1000 genomes]
rs7803374	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7805035	0.85[EUR][1000 genomes]
rs7810017	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997988	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998357	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv606432	chr7:25988185-26223294	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25987200-25993200	Active TSS	Pancreas	Pancrea
2	chr7:25987800-25992800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr7:25988000-25989600	Weak transcription	Right Atrium	heart
4	chr7:25988200-25990000	Flanking Active TSS	Liver	Liver
5	chr7:25988200-25990200	Flanking Active TSS	Duodenum Mucosa	Duodenum
6	chr7:25988400-25990200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:25988600-25989600	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr7:25988600-25989600	Enhancers	Lung	lung
9	chr7:25988800-25989600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr7:25988800-25989600	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr7:25988800-25989600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr7:25988800-25989600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:25988800-25989800	Flanking Active TSS	Thymus	Thymus
14	chr7:25989000-25989600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr7:25989000-25989600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr7:25989000-25989600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:25989000-25989600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr7:25989000-25989600	Enhancers	Small Intestine	intestine
19	chr7:25989000-25990000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr7:25989000-25990000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
21	chr7:25989000-25990000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr7:25989000-25990000	Flanking Active TSS	K562	blood
23	chr7:25989000-25990200	Flanking Active TSS	Fetal Thymus	thymus
24	chr7:25989000-25990200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr7:25989000-25991400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:25989200-25989600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:25989200-25989600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr7:25989200-25989600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:25989200-25989600	Flanking Active TSS	Fetal Lung	lung
30	chr7:25989200-25989600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
31	chr7:25989200-25989600	Flanking Active TSS	HepG2	liver
32	chr7:25989200-25989800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr7:25989200-25989800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
34	chr7:25989200-25990000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr7:25989200-25990000	Flanking Active TSS	NHEK	skin
36	chr7:25989200-25990200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr7:25989200-25990400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr7:25989200-25990400	Flanking Active TSS	Colonic Mucosa	Colon
39	chr7:25989200-25991400	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr7:25989200-25991600	Active TSS	Rectal Smooth Muscle	rectum
41	chr7:25989200-25992600	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr7:25989400-25989600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
43	chr7:25989400-25989600	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:25989400-25989600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr7:25989400-25989600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:25989400-25989600	Active TSS	Primary T cells from cord blood	blood
47	chr7:25989400-25989600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:25989400-25989600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:25989400-25989600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr7:25989400-25989600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links