Variant report

Variant	rs6790140
Chromosome Location	chr3:23984083-23984084
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
2	chr3:23930082..23933040-chr3:23982116..23985334,3	K562	blood:
3	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174748	Chromatin interaction
ENSG00000197885	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10084748	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037635	1.00[ASN][1000 genomes]
rs11129128	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070128	1.00[ASN][1000 genomes]
rs13087250	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316457	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317815	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13321439	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13321440	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1533141	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1567579	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567580	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524116	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34036067	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34058540	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082882	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593533	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34866549	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953164	1.00[ASN][1000 genomes]
rs35136361	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35457462	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35755171	1.00[ASN][1000 genomes]
rs35755253	1.00[ASN][1000 genomes]
rs36063721	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089963	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762775	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935253	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131404	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300960	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490300	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535169	1.00[ASN][1000 genomes]
rs4602333	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858096	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858554	1.00[ASN][1000 genomes]
rs4858556	1.00[ASN][1000 genomes]
rs4858564	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932805	1.00[ASN][1000 genomes]
rs6550808	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66609380	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67002637	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236598	1.00[ASN][1000 genomes]
rs67606949	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767005	1.00[ASN][1000 genomes]
rs6770052	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6775878	1.00[ASN][1000 genomes]
rs6776201	1.00[ASN][1000 genomes]
rs6776568	1.00[ASN][1000 genomes]
rs6778577	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6791805	1.00[ASN][1000 genomes]
rs6803214	1.00[ASN][1000 genomes]
rs6803587	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71324126	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150266	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150299	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610689	1.00[ASN][1000 genomes]
rs7610935	1.00[ASN][1000 genomes]
rs7611018	1.00[ASN][1000 genomes]
rs954748	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809225	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812419	1.00[ASN][1000 genomes]
rs9812870	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9817923	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9853954	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855481	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859567	1.00[ASN][1000 genomes]
rs9863176	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875577	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882067	1.00[ASN][1000 genomes]
rs9883834	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	esv3341907	chr3:23984076-23984451	Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23962000-23985600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:23964200-23985000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr3:23976800-23985600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:23979000-23985200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:23979000-23985400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:23979200-23985600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:23980400-23985200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:23980400-23985800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:23980600-23985200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:23980600-23985200	Weak transcription	Fetal Lung	lung
11	chr3:23980800-23985200	Weak transcription	Fetal Heart	heart
12	chr3:23982200-23986000	Weak transcription	Right Atrium	heart
13	chr3:23983200-23985200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:23983400-23985200	Weak transcription	K562	blood

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