Variant report

Variant	rs17685277
Chromosome Location	chr6:56823425-56823426
allele	C/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	GATA3	chr6:56823002-56825409	SK-N-SH	brain:	n/a	chr6:56825367-56825378 chr6:56823065-56823076 chr6:56824103-56824120 chr6:56824114-56824121 chr6:56824112-56824121 chr6:56825224-56825245 chr6:56824112-56824122 chr6:56824780-56824787 chr6:56824107-56824128 chr6:56824114-56824124
2	TCF12	chr6:56823140-56825363	SK-N-SH	brain:	n/a	n/a
3	YY1	chr6:56823328-56823818	SK-N-SH_RA	brain:	n/a	n/a
4	MEF2A	chr6:56823208-56824441	SK-N-SH	brain:	n/a	chr6:56823235-56823243 chr6:56824091-56824106
5	POLR2A	chr6:56823334-56823748	U87	brain:	n/a	n/a
6	JUND	chr6:56823144-56824481	SK-N-SH	brain:	n/a	chr6:56824309-56824318
7	GATA3	chr6:56823126-56825314	SK-N-SH	brain:	n/a	chr6:56824103-56824120 chr6:56824114-56824121 chr6:56824112-56824121 chr6:56825224-56825245 chr6:56824112-56824122 chr6:56824780-56824787 chr6:56824107-56824128 chr6:56824114-56824124
8	POLR2A	chr6:56823238-56823745	SK-N-SH	brain:	n/a	n/a
9	PBX3	chr6:56823132-56824529	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr6:56823153-56823812	U87	brain:	n/a	n/a
11	PBX3	chr6:56823295-56824488	SK-N-SH	brain:	n/a	n/a
12	JUND	chr6:56823195-56825353	SK-N-SH	brain:	n/a	chr6:56824945-56824955 chr6:56824946-56824954 chr6:56824945-56824955 chr6:56824945-56824955 chr6:56824944-56824955 chr6:56824309-56824318 chr6:56824947-56824954 chr6:56824946-56824954
13	EP300	chr6:56823094-56825315	SK-N-SH	brain:	n/a	chr6:56824945-56824954 chr6:56823231-56823245 chr6:56823712-56823726
14	EP300	chr6:56823233-56824375	SK-N-SH	brain:	n/a	chr6:56823712-56823726
15	EP300	chr6:56823413-56823739	SK-N-SH_RA	brain:	n/a	chr6:56823712-56823726
16	EP300	chr6:56823299-56825362	SK-N-SH	brain:	n/a	chr6:56824945-56824954 chr6:56823712-56823726
17	TEAD4	chr6:56823195-56825336	SK-N-SH	brain:	n/a	n/a
18	FOSL2	chr6:56823192-56824418	SK-N-SH	brain:	n/a	chr6:56824309-56824318
19	MAX	chr6:56823234-56823790	SK-N-SH	brain:	n/a	n/a
20	JUND	chr6:56823205-56824415	SK-N-SH	brain:	n/a	chr6:56824309-56824318
21	RXRA	chr6:56823170-56824485	SK-N-SH	brain:	n/a	n/a
22	NFIC	chr6:56823125-56825365	SK-N-SH	brain:	n/a	n/a
23	TCF12	chr6:56823016-56825265	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:56819016..56821758-chr6:56822095..56823994,2	K562	blood:
2	chr6:56821886..56823483-chr6:56846659..56848373,2	MCF-7	breast:
3	chr6:56813560..56816424-chr6:56821895..56824578,2	K562	blood:
4	chr6:56821970..56823839-chr6:57043056..57044628,2	K562	blood:
5	chr6:56817498..56822021-chr6:56822095..56825634,7	MCF-7	breast:

Variant related genes	Relation type
DST	TF binding region
ENSG00000151917	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1007417	0.84[TSI][hapmap]
rs1020548	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1044670	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs13193465	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13193800	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13195825	0.93[AFR][1000 genomes]
rs13198484	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13203600	0.93[AFR][1000 genomes]
rs13205022	0.93[AFR][1000 genomes]
rs13207768	1.00[ASW][hapmap]
rs13207800	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13209099	0.93[AFR][1000 genomes]
rs13212013	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13214255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13215865	1.00[AFR][1000 genomes]
rs13216793	0.93[AFR][1000 genomes]
rs13218276	0.91[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13220510	1.00[AFR][1000 genomes]
rs13220575	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1451707	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1451708	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1460561	1.00[AFR][1000 genomes]
rs1562908	0.84[TSI][hapmap]
rs1599280	1.00[ASW][hapmap];1.00[GIH][hapmap]
rs17685143	1.00[AFR][1000 genomes]
rs17685338	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17685380	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1903330	1.00[LWK][hapmap];1.00[AFR][1000 genomes]
rs2397227	0.84[TSI][hapmap]
rs2613119	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2817573	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360535	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28360536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28360538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34009699	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34027274	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34232358	1.00[AFR][1000 genomes]
rs34399458	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34616943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34714091	1.00[AFR][1000 genomes]
rs34733863	1.00[AFR][1000 genomes]
rs34812189	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs34979183	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35090265	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35336675	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35434542	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs35605425	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35735810	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35899012	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35961728	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs36112505	1.00[AFR][1000 genomes]
rs36124814	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3957366	1.00[ASW][hapmap]
rs55952713	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56381984	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6901944	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6904172	0.84[TSI][hapmap]
rs6904924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6906623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6907143	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6927558	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71550519	1.00[AFR][1000 genomes]
rs71564866	1.00[AFR][1000 genomes]
rs71564868	0.87[AFR][1000 genomes]
rs71564869	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564870	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564872	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs720884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs720885	0.84[TSI][hapmap]
rs7760385	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382669	0.84[TSI][hapmap]
rs9382670	0.84[TSI][hapmap]
rs9396246	0.84[TSI][hapmap]
rs9396250	0.84[TSI][hapmap]
rs9475758	0.84[TSI][hapmap]
rs9475760	0.84[TSI][hapmap]
rs9475763	0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs17685277	BEND6	cis	Heart Left Ventricle	GTEx
rs17685277	DST	cis	cerebellum	SCAN
rs17685277	RAB23	cis	multi-tissue	Pritchard
rs17685277	BEND6	cis	Artery Tibial	GTEx
rs17685277	BEND6	cis	Thyroid	GTEx
rs17685277	BEND6	cis	Esophagus Mucosa	GTEx
rs17685277	C6orf65	cis	multi-tissue	Pritchard
rs17685277	BEND6	cis	parietal	SCAN
rs17685277	BEND6	cis	cerebellum	SCAN
rs17685277	BEND6	cis	Esophagus Muscularis	GTEx
rs17685277	BEND6	cis	Muscle Skeletal	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56821000-56824600	Weak transcription	HSMMtube	muscle
2	chr6:56821000-56824600	Weak transcription	HUVEC	blood vessel
3	chr6:56821200-56823600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:56821600-56823600	Enhancers	NHDF-Ad	bronchial
5	chr6:56821600-56823800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:56821600-56823800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:56821600-56824000	Weak transcription	HMEC	breast
8	chr6:56821600-56824000	Weak transcription	NHEK	skin
9	chr6:56822800-56823600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:56822800-56824400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:56822800-56824600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:56822800-56825200	Enhancers	NH-A	brain
13	chr6:56822800-56825400	Enhancers	HSMM	muscle
14	chr6:56822800-56825600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:56822800-56826200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:56822800-56826200	Enhancers	NHLF	lung
17	chr6:56823000-56824600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:56823000-56824600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr6:56823000-56825400	Enhancers	Hela-S3	cervix
20	chr6:56823000-56828000	Enhancers	Osteobl	bone
21	chr6:56823400-56824000	Weak transcription	K562	blood
22	chr6:56823400-56824200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:56823400-56824600	Enhancers	A549	lung

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