Variant report

Variant	rs6490282
Chromosome Location	chr12:120503322-120503323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120502380..120507163-chr12:120508034..120511527,6	K562	blood:
2	chr12:120475158..120477800-chr12:120503210..120505823,2	K562	blood:
3	chr12:120502350..120506477-chr12:120508342..120509946,3	K562	blood:
4	chr12:120500334..120503561-chr12:120515815..120519326,4	MCF-7	breast:
5	chr12:120502778..120504935-chr12:120729246..120731977,2	MCF-7	breast:
6	chr12:120497978..120500428-chr12:120503255..120504973,2	K562	blood:

Variant related genes	Relation type
ENSG00000135127	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1054631	1.00[ASN][1000 genomes]
rs16949854	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949862	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949870	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949914	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286041	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613380	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56105460	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56152568	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56939014	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57155388	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57339959	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57458743	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59868595	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59911114	0.93[EUR][1000 genomes]
rs60106911	1.00[ASN][1000 genomes]
rs60223336	1.00[ASN][1000 genomes]
rs60590470	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60742518	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61514727	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490279	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7132099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7139151	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7297564	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298081	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304560	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956221	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957325	1.00[AMR][1000 genomes];0.85[EUR][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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120486800-120512000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:120487800-120512200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:120493800-120523800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:120494800-120517800	Weak transcription	Lung	lung
5	chr12:120497600-120507400	Enhancers	Stomach Mucosa	stomach
6	chr12:120497600-120509400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:120498200-120507400	Strong transcription	Primary T cells from cord blood	blood
8	chr12:120498400-120511600	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr12:120498600-120503600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:120498600-120504200	Enhancers	Brain Angular Gyrus	brain
11	chr12:120498800-120516600	Weak transcription	Fetal Brain Male	brain
12	chr12:120499200-120504600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:120499200-120506000	Strong transcription	Thymus	Thymus
14	chr12:120499200-120507800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:120499400-120503600	Enhancers	HepG2	liver
16	chr12:120499400-120505400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr12:120499400-120506400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr12:120499400-120509400	Weak transcription	Pancreas	Pancrea
19	chr12:120499800-120511200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:120499800-120516400	Weak transcription	Primary B cells from cord blood	blood
21	chr12:120500200-120503600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:120501000-120504800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:120501600-120503800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr12:120502000-120506600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:120502000-120523400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr12:120502200-120503600	Enhancers	Brain Cingulate Gyrus	brain
27	chr12:120502200-120505800	Weak transcription	Right Ventricle	heart
28	chr12:120502200-120509600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr12:120502200-120509600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:120502200-120516600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr12:120502200-120517800	Weak transcription	Gastric	stomach
32	chr12:120502400-120503400	Strong transcription	Fetal Thymus	thymus
33	chr12:120502400-120503600	Enhancers	Brain Hippocampus Middle	brain
34	chr12:120502400-120503600	Strong transcription	Esophagus	oesophagus
35	chr12:120502400-120503600	Strong transcription	Fetal Brain Female	brain
36	chr12:120502400-120503800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:120502400-120504200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:120502400-120504600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:120502400-120505800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:120502400-120505800	Weak transcription	Right Atrium	heart
41	chr12:120502400-120523200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:120502400-120523400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:120502400-120524400	Weak transcription	Fetal Intestine Small	intestine
44	chr12:120502600-120503800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr12:120502600-120503800	Enhancers	Liver	Liver
46	chr12:120502600-120504000	Weak transcription	NHEK	skin
47	chr12:120502600-120505400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:120502600-120507200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:120502600-120518400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr12:120502600-120524400	Weak transcription	Brain Anterior Caudate	brain

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