Variant report

Variant	rs17171630
Chromosome Location	chr7:39961809-39961810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39961241..39963014-chr7:39971580..39973102,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10228050	1.00[EUR][1000 genomes]
rs10236585	1.00[EUR][1000 genomes]
rs10241287	1.00[EUR][1000 genomes]
rs10241835	1.00[EUR][1000 genomes]
rs10244506	1.00[EUR][1000 genomes]
rs10256280	1.00[EUR][1000 genomes]
rs10256385	1.00[EUR][1000 genomes]
rs10257242	1.00[EUR][1000 genomes]
rs10258115	1.00[EUR][1000 genomes]
rs10259564	1.00[EUR][1000 genomes]
rs10267751	1.00[EUR][1000 genomes]
rs10270724	1.00[EUR][1000 genomes]
rs10271401	1.00[EUR][1000 genomes]
rs10275367	1.00[EUR][1000 genomes]
rs1060299	1.00[EUR][1000 genomes]
rs17171639	1.00[EUR][1000 genomes]
rs17171643	1.00[EUR][1000 genomes]
rs17171644	1.00[EUR][1000 genomes]
rs17171648	1.00[EUR][1000 genomes]
rs17171649	1.00[EUR][1000 genomes]
rs17496395	1.00[EUR][1000 genomes]
rs17537831	1.00[EUR][1000 genomes]
rs17538020	1.00[EUR][1000 genomes]
rs28374865	1.00[EUR][1000 genomes]
rs28714188	1.00[EUR][1000 genomes]
rs28823992	1.00[EUR][1000 genomes]
rs56885787	1.00[EUR][1000 genomes]
rs56890877	1.00[EUR][1000 genomes]
rs57300694	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57667402	1.00[EUR][1000 genomes]
rs57765448	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58664547	0.93[AFR][1000 genomes]
rs58787667	1.00[EUR][1000 genomes]
rs59146346	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59537889	1.00[EUR][1000 genomes]
rs59749446	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60101070	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60615872	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60806836	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61635237	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6462957	1.00[EUR][1000 genomes]
rs6462958	1.00[EUR][1000 genomes]
rs6462960	1.00[EUR][1000 genomes]
rs6946176	1.00[EUR][1000 genomes]
rs6953989	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6955589	1.00[EUR][1000 genomes]
rs6958792	1.00[EUR][1000 genomes]
rs6964473	1.00[EUR][1000 genomes]
rs6965022	1.00[EUR][1000 genomes]
rs6973262	1.00[EUR][1000 genomes]
rs6976377	1.00[EUR][1000 genomes]
rs73381425	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73381433	0.94[AFR][1000 genomes]
rs73381435	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73381438	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73381440	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73381442	0.94[AFR][1000 genomes]
rs73381453	1.00[EUR][1000 genomes]
rs73392765	1.00[EUR][1000 genomes]
rs7794028	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7809754	1.00[EUR][1000 genomes]
rs9655408	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	esv3375265	chr7:39939761-39966001	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3347596	chr7:39939761-39969926	Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39950000-39965000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:39960600-39962000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr7:39960600-39962000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:39960600-39962000	Enhancers	Fetal Muscle Trunk	muscle
5	chr7:39960600-39962000	Enhancers	Fetal Muscle Leg	muscle
6	chr7:39961000-39962600	Enhancers	HepG2	liver
7	chr7:39961400-39962000	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr7:39961800-39962000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr7:39961800-39963000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:39961800-39963000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:39961800-39964800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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