Variant report

Variant	rs12476289
Chromosome Location	chr2:179641975-179641976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179641847..179643988-chr2:179646458..179648017,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10171049	0.84[ASN][1000 genomes]
rs11902709	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12464157	1.00[AFR][1000 genomes]
rs12464703	0.86[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12470905	0.87[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12476203	1.00[AFR][1000 genomes]
rs12477340	1.00[AFR][1000 genomes]
rs16866497	1.00[GIH][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16866532	0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17453396	1.00[AFR][1000 genomes]
rs17453403	1.00[AFR][1000 genomes]
rs1883084	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1883085	1.00[GIH][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2253324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2291304	0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291305	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291308	0.87[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291309	0.90[ASN][1000 genomes]
rs2291310	0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs2291311	0.80[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2291312	0.80[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2306636	0.87[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2562829	1.00[GIH][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2627040	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2627041	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2742347	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2742357	1.00[GIH][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3754953	0.84[ASN][1000 genomes]
rs3769860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4894037	0.84[ASN][1000 genomes]
rs55863869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55913885	1.00[AFR][1000 genomes]
rs56030306	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56120016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56142888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66677602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72647839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72647889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72648917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7585334	0.84[ASN][1000 genomes]
rs7604033	0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs922984	0.84[ASN][1000 genomes]
rs966783	1.00[AFR][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	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv962089	chr2:179635536-179643793	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

Variant related diseases (count:1)

Disease	PMID	Source
QT interval	20031603	GWAS catalog

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:179605400-179662400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:179610800-179671400	Weak transcription	Ovary	ovary
4	chr2:179614200-179645200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:179627000-179655200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:179627400-179653200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:179627600-179652600	Weak transcription	Brain Substantia Nigra	brain
8	chr2:179627600-179663800	Weak transcription	Thymus	Thymus
9	chr2:179629600-179666200	Weak transcription	GM12878-XiMat	blood
10	chr2:179630600-179651000	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:179631200-179649800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:179632000-179658800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:179632400-179667800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:179634200-179648600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:179634400-179645200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:179636200-179643000	Weak transcription	HSMM	muscle
17	chr2:179636200-179647000	Weak transcription	Lung	lung
18	chr2:179636200-179660600	Weak transcription	Brain Anterior Caudate	brain
19	chr2:179637200-179651000	Strong transcription	Primary T cells from cord blood	blood
20	chr2:179637200-179651000	Strong transcription	HSMMtube	muscle
21	chr2:179637400-179643800	Strong transcription	Primary B cells from cord blood	blood
22	chr2:179637600-179647000	Strong transcription	Fetal Muscle Leg	muscle
23	chr2:179639000-179672000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:179639400-179671400	Weak transcription	Gastric	stomach
25	chr2:179639600-179642800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:179640000-179644000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:179640400-179643600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:179640600-179644800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr2:179640800-179642600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr2:179640800-179642800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:179641000-179642400	Strong transcription	Fetal Thymus	thymus
32	chr2:179641000-179644000	Strong transcription	Left Ventricle	heart
33	chr2:179641200-179644800	Weak transcription	Psoas Muscle	Psoas
34	chr2:179641200-179645400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:179641400-179642600	Strong transcription	Fetal Heart	heart
36	chr2:179641400-179642600	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:179641600-179642000	Weak transcription	Fetal Intestine Large	intestine
38	chr2:179641600-179642800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr2:179641600-179647400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:179641800-179643400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:179641800-179646800	Weak transcription	Pancreas	Pancrea
42	chr2:179641800-179646800	Weak transcription	Right Ventricle	heart
43	chr2:179641800-179647000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr2:179641800-179648800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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