Variant report

Variant	rs12699419
Chromosome Location	chr7:12854268-12854269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:12853166..12855784-chr7:12857906..12859818,2	K562	blood:
2	chr7:12725132..12728581-chr7:12853951..12856846,4	K562	blood:
3	chr7:12853864..12855585-chr7:12855723..12857729,3	K562	blood:
4	chr7:12844977..12847724-chr7:12851734..12854680,3	K562	blood:
5	chr7:12847834..12849363-chr7:12852693..12855158,2	K562	blood:
6	chr7:12757666..12759532-chr7:12853077..12856020,2	K562	blood:
7	chr7:12848902..12851417-chr7:12852205..12854551,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122644	Chromatin interaction
ENSG00000271253	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10233379	0.90[EUR][1000 genomes]
rs10235332	0.90[EUR][1000 genomes]
rs10237365	0.90[EUR][1000 genomes]
rs10950417	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950418	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950419	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11495996	1.00[ASN][1000 genomes]
rs12155420	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216561	1.00[ASN][1000 genomes]
rs12530804	1.00[ASN][1000 genomes]
rs12531011	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531228	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531814	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12532172	1.00[ASN][1000 genomes]
rs12533247	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533314	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533912	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533952	0.88[EUR][1000 genomes]
rs12534712	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535230	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535869	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536932	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538097	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538194	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538763	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12538792	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539313	0.88[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539387	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539416	1.00[ASN][1000 genomes]
rs12540042	1.00[ASN][1000 genomes]
rs12699416	0.83[CEU][hapmap];0.80[AMR][1000 genomes]
rs12699417	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12699421	0.94[EUR][1000 genomes]
rs12699422	0.95[EUR][1000 genomes]
rs12699426	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12699432	1.00[ASN][1000 genomes]
rs12699433	1.00[ASN][1000 genomes]
rs13222073	0.83[EUR][1000 genomes]
rs13222475	0.82[EUR][1000 genomes]
rs13224587	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13225356	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13225358	0.82[EUR][1000 genomes]
rs13227946	1.00[ASN][1000 genomes]
rs13228110	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13228635	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232299	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13233019	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13233170	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13233911	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13235201	1.00[ASN][1000 genomes]
rs13236001	1.00[ASN][1000 genomes]
rs13236020	0.84[CEU][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238922	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13244444	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504348	0.97[EUR][1000 genomes]
rs34057597	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34107937	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34269223	0.90[EUR][1000 genomes]
rs34338066	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34488685	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34529424	1.00[ASN][1000 genomes]
rs34591294	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34755449	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34809518	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34904008	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34928291	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34971219	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35003906	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35181098	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35193720	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35290407	0.97[EUR][1000 genomes]
rs35464195	0.82[EUR][1000 genomes]
rs35616205	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35769393	1.00[ASN][1000 genomes]
rs35859074	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35867430	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35917995	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35942853	1.00[ASN][1000 genomes]
rs35966640	1.00[ASN][1000 genomes]
rs35988890	0.95[EUR][1000 genomes]
rs36003929	0.95[EUR][1000 genomes]
rs36091229	0.94[EUR][1000 genomes]
rs55864529	0.83[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55943442	1.00[ASN][1000 genomes]
rs62445836	0.82[EUR][1000 genomes]
rs62450583	1.00[ASN][1000 genomes]
rs6954306	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954419	0.95[EUR][1000 genomes]
rs71536902	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71538805	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71538808	1.00[ASN][1000 genomes]
rs9647958	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9648162	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
4	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
5	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
6	esv2422346	chr7:12739291-12883550	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1027501	chr7:12743592-12927109	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv606235	chr7:12781381-13205950	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1020568	chr7:12802640-13183737	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1027806	chr7:12842708-12875714	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
11	nsv1016775	chr7:12845004-12865643	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
12	nsv981801	chr7:12848501-12854945	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12845800-12854400	Weak transcription	K562	blood
2	chr7:12846800-12854800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr7:12849600-12854400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:12850000-12856800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:12853200-12854800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:12853200-12854800	Enhancers	HMEC	breast
7	chr7:12853200-12855200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:12853600-12854400	Flanking Active TSS	NHEK	skin
9	chr7:12853800-12854600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr7:12853800-12857200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr7:12854000-12855800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr7:12854200-12854400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr7:12854200-12854600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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