Variant report

Variant	rs12538097
Chromosome Location	chr7:12840867-12840868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:12839807..12841884-chr7:12848614..12851118,2	K562	blood:
2	chr7:12835963..12838649-chr7:12840426..12842028,2	K562	blood:
3	chr7:12829364..12832120-chr7:12840009..12842222,2	MCF-7	breast:
4	chr7:12839996..12842956-chr7:12845077..12847690,3	K562	blood:
5	chr7:12753064..12757665-chr7:12839772..12843667,5	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10233379	0.89[EUR][1000 genomes]
rs10235332	0.89[EUR][1000 genomes]
rs10237365	0.89[EUR][1000 genomes]
rs10950417	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950418	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950419	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11495996	1.00[ASN][1000 genomes]
rs12155420	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216561	1.00[ASN][1000 genomes]
rs12530804	1.00[ASN][1000 genomes]
rs12531011	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531228	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531814	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12532172	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12533247	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533314	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533912	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533952	0.89[EUR][1000 genomes]
rs12534712	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535230	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535869	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536932	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538194	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538763	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12538792	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539313	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539387	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539416	1.00[ASN][1000 genomes]
rs12540042	1.00[ASN][1000 genomes]
rs12699416	0.88[CEU][hapmap];0.88[AMR][1000 genomes]
rs12699417	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12699419	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12699421	0.93[EUR][1000 genomes]
rs12699422	0.94[EUR][1000 genomes]
rs12699426	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12699432	1.00[ASN][1000 genomes]
rs12699433	1.00[ASN][1000 genomes]
rs13222073	0.82[EUR][1000 genomes]
rs13222475	0.81[EUR][1000 genomes]
rs13224587	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13225356	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13225358	0.81[EUR][1000 genomes]
rs13227946	1.00[ASN][1000 genomes]
rs13228110	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13228635	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13232299	0.93[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13233019	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13233170	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13233911	1.00[AFR][1000 genomes];0.98[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];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238922	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13244444	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504348	0.96[EUR][1000 genomes]
rs34057597	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34107937	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34269223	0.89[EUR][1000 genomes]
rs34338066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34488685	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34529424	1.00[ASN][1000 genomes]
rs34591294	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34755449	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34809518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34904008	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34928291	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34971219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35003906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35181098	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35193720	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35290407	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35464195	0.81[EUR][1000 genomes]
rs35616205	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35769393	1.00[ASN][1000 genomes]
rs35859074	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35867430	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35917995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35942853	1.00[ASN][1000 genomes]
rs35966640	1.00[ASN][1000 genomes]
rs35988890	0.94[EUR][1000 genomes]
rs36003929	0.94[EUR][1000 genomes]
rs36091229	0.93[EUR][1000 genomes]
rs55864529	0.83[AFR][1000 genomes];0.96[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	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6954419	0.94[EUR][1000 genomes]
rs71536902	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71538805	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71538808	1.00[ASN][1000 genomes]
rs9647958	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9648162	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv606236	chr7:12791487-12846898	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	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
11	nsv521756	chr7:12840090-12852124	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12834800-12841800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:12838400-12844200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr7:12839000-12845600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:12839800-12843000	Enhancers	Fetal Intestine Small	intestine
5	chr7:12840000-12841400	Enhancers	HSMM	muscle
6	chr7:12840000-12842200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr7:12840000-12843400	Enhancers	Fetal Intestine Large	intestine
8	chr7:12840200-12842000	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr7:12840200-12842200	Enhancers	Placenta	Placenta
10	chr7:12840200-12842600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:12840200-12842600	Enhancers	K562	blood
12	chr7:12840200-12843000	Enhancers	HMEC	breast
13	chr7:12840200-12843000	Enhancers	NHEK	skin
14	chr7:12840200-12843400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:12840400-12841200	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr7:12840400-12842800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:12840600-12842200	Enhancers	HSMMtube	muscle
18	chr7:12840600-12842800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr7:12840800-12841000	Flanking Active TSS	Duodenum Mucosa	Duodenum
20	chr7:12840800-12841000	Enhancers	Esophagus	oesophagus
21	chr7:12840800-12841000	Enhancers	Right Atrium	heart
22	chr7:12840800-12841000	Enhancers	A549	lung
23	chr7:12840800-12841400	Active TSS	Stomach Mucosa	stomach
24	chr7:12840800-12842200	Enhancers	Pancreas	Pancrea

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