Variant report

Variant	rs17258907
Chromosome Location	chr4:119769905-119769906
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119756043..119758170-chr4:119769333..119772030,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10001115	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10018977	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10019311	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10025640	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11098451	0.80[CEU][hapmap]
rs11938970	0.80[CEU][hapmap]
rs17257039	0.89[CEU][hapmap]
rs17257945	0.80[CEU][hapmap]
rs17258050	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs17258106	0.80[CEU][hapmap]
rs17258830	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs17259173	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17259257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17259284	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17323012	0.80[CEU][hapmap]
rs17323034	0.80[CEU][hapmap]
rs17323877	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs17324807	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17324821	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17324884	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17324968	0.89[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17325017	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17325129	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17325192	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28797314	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28837152	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs41455648	0.80[CEU][hapmap];1.00[AFR][1000 genomes]
rs55633605	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55640619	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55649377	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55668908	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55671478	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55704595	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55726697	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55744948	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55758547	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55794497	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55806110	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55823625	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55869953	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55901549	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55913633	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55985953	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56027489	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56046449	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56046676	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56055826	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56104443	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56117870	0.92[AMR][1000 genomes]
rs56124677	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56144225	1.00[AFR][1000 genomes]
rs56150431	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56162974	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56212415	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56227053	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56252481	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56264833	0.85[AMR][1000 genomes]
rs56283736	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56291421	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56302493	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56302600	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56303276	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs56309519	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56322132	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56331118	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56342843	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56359736	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56364904	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56388366	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56389935	1.00[AFR][1000 genomes]
rs56762141	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6818519	0.83[EUR][1000 genomes]
rs73842253	0.83[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	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3376985	chr4:119757182-119774736	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119758200-119771200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:119762800-119771400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:119764000-119771000	Weak transcription	NHDF-Ad	bronchial
4	chr4:119764000-119771200	Weak transcription	NHEK	skin
5	chr4:119764000-119771200	Weak transcription	Osteobl	bone
6	chr4:119764000-119771600	Weak transcription	HSMM	muscle
7	chr4:119764800-119771400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:119764800-119771600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:119764800-119771800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr4:119767000-119771400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:119768600-119770000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:119768600-119770200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr4:119769600-119770000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr4:119769600-119770200	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr4:119769600-119770800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr4:119769600-119771400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:119769800-119770400	Enhancers	H9 Cell Line	embryonic stem cell
18	chr4:119769800-119770400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr4:119769800-119770600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr4:119769800-119770600	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr4:119769800-119770800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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