Variant report

Variant	rs6961040
Chromosome Location	chr7:39977247-39977248
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	chr7:39975051..39978175-chr7:39986837..39989689,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259826	Chromatin interaction
ENSG00000065883	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1002749	0.89[ASN][1000 genomes]
rs10232503	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10233552	0.84[EUR][1000 genomes]
rs10243593	0.93[ASN][1000 genomes]
rs10252631	0.84[EUR][1000 genomes]
rs10261984	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10951623	0.87[EUR][1000 genomes]
rs10951624	0.84[EUR][1000 genomes]
rs10951625	0.87[EUR][1000 genomes]
rs11768464	0.93[ASN][1000 genomes]
rs11972983	0.87[EUR][1000 genomes]
rs11977756	0.87[EUR][1000 genomes]
rs11983287	0.87[EUR][1000 genomes]
rs12530835	0.87[EUR][1000 genomes]
rs12531761	0.87[EUR][1000 genomes]
rs12531774	0.87[EUR][1000 genomes]
rs12532714	0.84[EUR][1000 genomes]
rs12534103	0.84[EUR][1000 genomes]
rs12535281	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12536190	0.87[EUR][1000 genomes]
rs12536349	0.82[EUR][1000 genomes]
rs12536726	0.87[EUR][1000 genomes]
rs12537125	0.87[EUR][1000 genomes]
rs12537320	0.87[EUR][1000 genomes]
rs12539956	0.84[EUR][1000 genomes]
rs1257698	0.84[EUR][1000 genomes]
rs12666454	0.89[EUR][1000 genomes]
rs12669872	0.87[EUR][1000 genomes]
rs12672040	0.84[EUR][1000 genomes]
rs12672136	0.87[EUR][1000 genomes]
rs12672142	0.87[EUR][1000 genomes]
rs13438258	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13438262	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13438324	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17171637	0.87[EUR][1000 genomes]
rs17171645	0.87[EUR][1000 genomes]
rs17171646	0.87[EUR][1000 genomes]
rs17496429	0.87[EUR][1000 genomes]
rs17496670	0.84[EUR][1000 genomes]
rs17496733	0.87[EUR][1000 genomes]
rs17537767	0.87[EUR][1000 genomes]
rs17538125	0.87[EUR][1000 genomes]
rs2015842	0.87[EUR][1000 genomes]
rs2159489	0.81[EUR][1000 genomes]
rs2302341	0.87[EUR][1000 genomes]
rs2329615	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28627647	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28879668	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34650758	0.88[ASN][1000 genomes]
rs35915527	0.81[ASN][1000 genomes]
rs3735135	0.87[EUR][1000 genomes]
rs3800799	0.86[EUR][1000 genomes]
rs3801238	0.86[EUR][1000 genomes]
rs3847019	0.87[EUR][1000 genomes]
rs3911836	0.87[EUR][1000 genomes]
rs3911889	0.87[EUR][1000 genomes]
rs4344004	0.87[EUR][1000 genomes]
rs4720344	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720347	0.84[EUR][1000 genomes]
rs4720349	0.84[EUR][1000 genomes]
rs4723923	0.87[EUR][1000 genomes]
rs4723925	0.84[EUR][1000 genomes]
rs4723927	0.87[EUR][1000 genomes]
rs4723928	0.87[EUR][1000 genomes]
rs60315659	0.87[EUR][1000 genomes]
rs6462956	0.95[ASN][1000 genomes]
rs6956091	0.89[ASN][1000 genomes]
rs6963973	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6967332	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6970469	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs758696	0.87[EUR][1000 genomes]
rs773411	0.84[EUR][1000 genomes]
rs7779663	0.87[EUR][1000 genomes]
rs7790624	0.93[ASN][1000 genomes]
rs940272	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39976600-39977600	Enhancers	NHEK	skin
2	chr7:39976600-39977800	Enhancers	HMEC	breast
3	chr7:39976800-39977800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:39977200-39977600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:39977200-39977800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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