Variant report

Variant	rs12540556
Chromosome Location	chr7:12713516-12713517
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	chr7:12713108..12716058-chr7:13259369..13262315,2	K562	blood:
2	chr7:12713078..12715028-chr7:12724717..12726950,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VWDE-3	chr7:12713477-12713925	XLOC_006356

Variant related genes	Relation type
ENSG00000271253	Chromatin interaction
ENSG00000122644	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10246960	0.82[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap]
rs10247152	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10279548	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279649	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280332	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13226084	0.82[CHB][hapmap]
rs2241748	0.86[GIH][hapmap]
rs35407540	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66871471	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67302850	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6944823	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73053437	0.81[ASN][1000 genomes]
rs73053442	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73053448	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73053455	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73053467	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73053491	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73053493	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73053495	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73053498	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73053502	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1017577	chr7:12530491-12722947	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv830907	chr7:12661239-12818250	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv932020	chr7:12676890-13239551	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv830908	chr7:12695007-12870475	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv1794967	chr7:12710385-12758624	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	n/a
8	nsv868830	chr7:12712753-13517417	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12711400-12714600	Weak transcription	Primary B cells from peripheral blood	blood
2	chr7:12712800-12715000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr7:12713000-12713800	Enhancers	Primary B cells from cord blood	blood
4	chr7:12713200-12713600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr7:12713200-12715000	Enhancers	NHEK	skin
6	chr7:12713400-12714800	Weak transcription	Placenta	Placenta

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