Variant report

Variant	rs12206564
Chromosome Location	chr6:100987009-100987010
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10457808	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10457809	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10782302	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs108422	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11155496	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11155498	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12190903	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12191199	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12192249	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12200565	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12206182	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12206945	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12374612	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12660725	0.92[CEU][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs151638	0.81[AMR][1000 genomes]
rs17303769	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1875400	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1875401	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2001102	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2062634	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2062635	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239234	0.81[AMR][1000 genomes]
rs239236	0.81[AMR][1000 genomes]
rs2398132	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs240111	0.83[ASN][1000 genomes]
rs240115	0.84[AMR][1000 genomes]
rs240164	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs240764	0.81[EUR][1000 genomes]
rs240765	0.81[EUR][1000 genomes]
rs240772	0.80[EUR][1000 genomes]
rs240776	0.81[EUR][1000 genomes]
rs395521	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4461738	0.92[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs454747	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62422675	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023710	chr6:100810738-101001115	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv538388	chr6:100810738-101001115	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv886444	chr6:100961198-101084946	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv604263	chr6:100980874-101078718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:100952800-100997400	Weak transcription	A549	lung
2	chr6:100955800-100991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:100957400-100992400	Weak transcription	Small Intestine	intestine
4	chr6:100960600-100990200	Weak transcription	Brain Substantia Nigra	brain
5	chr6:100960800-100989600	Weak transcription	K562	blood
6	chr6:100960800-100989800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:100960800-101035000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:100961000-100987200	Weak transcription	Osteobl	bone
9	chr6:100961000-100988800	Weak transcription	NHEK	skin
10	chr6:100961000-100991200	Weak transcription	HSMMtube	muscle
11	chr6:100961000-100992000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:100961000-100997200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:100961200-100989000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:100964000-100990800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:100964200-101020000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:100964800-100998400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:100965200-100989600	Weak transcription	Aorta	Aorta
18	chr6:100965200-100990200	Weak transcription	Left Ventricle	heart
19	chr6:100965200-101000800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:100965200-101011400	Weak transcription	Pancreas	Pancrea
21	chr6:100965400-100988600	Weak transcription	Lung	lung
22	chr6:100965400-100989600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:100965400-100989800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:100965400-100990400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr6:100965400-100991800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr6:100965400-101005000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:100965600-100987800	Weak transcription	Adipose Nuclei	Adipose
28	chr6:100965600-101033600	Weak transcription	Ovary	ovary
29	chr6:100965800-100987400	Weak transcription	Placenta	Placenta
30	chr6:100966000-101002400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:100966200-100991000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:100966200-100996800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:100969800-100988000	Weak transcription	Esophagus	oesophagus
34	chr6:100974400-100987600	Weak transcription	NH-A	brain
35	chr6:100978200-101008200	Weak transcription	NHDF-Ad	bronchial
36	chr6:100978600-100989800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:100978600-101019400	Weak transcription	HMEC	breast
38	chr6:100979000-100989600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:100979200-100991400	Weak transcription	Liver	Liver
40	chr6:100979800-101018200	Weak transcription	Primary T cells from cord blood	blood
41	chr6:100981800-100990000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr6:100981800-101001400	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:100983000-100989600	Strong transcription	Dnd41	blood
44	chr6:100984000-100988200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:100984200-100987600	Weak transcription	Fetal Thymus	thymus
46	chr6:100984200-100987600	Strong transcription	HSMM	muscle
47	chr6:100984400-100989000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:100984600-100987400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:100984800-100991200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr6:100984800-101000400	Weak transcription	HepG2	liver

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