Variant report

Variant	rs4758666
Chromosome Location	chr12:122902840-122902841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122902497..122904051-chr12:122964826..122966588,2	MCF-7	breast:
2	chr12:122879571..122888507-chr12:122899670..122909196,27	K562	blood:
3	chr12:122902575..122904900-chr12:122907634..122909136,2	MCF-7	breast:
4	chr12:122902285..122904972-chr12:122905751..122909798,4	K562	blood:
5	chr12:122902598..122904483-chr12:122905269..122908349,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257097	Chromatin interaction
ENSG00000033030	Chromatin interaction
ENSG00000130779	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10161534	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10734915	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10734918	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734924	0.88[JPT][hapmap]
rs10744192	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744208	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10744209	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744210	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744211	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744217	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10744220	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10744287	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs10773075	0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.89[TSI][hapmap]
rs10773088	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10773103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10773104	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10773152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs10773167	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773172	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10773176	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773178	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773208	0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs10846664	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs10846688	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs10846699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846764	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846792	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10846826	0.82[AMR][1000 genomes]
rs10846830	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846835	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10846920	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846921	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846931	0.87[EUR][1000 genomes]
rs10846978	0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs10847179	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs10847242	0.88[JPT][hapmap]
rs10998	0.85[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap]
rs11057786	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11057797	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057882	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11058034	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11058209	0.84[EUR][1000 genomes]
rs11058226	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058233	0.81[EUR][1000 genomes]
rs11058251	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11058402	0.85[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11616082	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11836188	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12369858	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs12372756	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12423420	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12425970	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12581249	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1473553	0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs1553179	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1803290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1818050	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1973463	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062488	0.89[CEU][hapmap];0.94[TSI][hapmap]
rs2173582	0.81[EUR][1000 genomes]
rs2341439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28730465	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34129612	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3817011	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs4039670	0.81[ASN][1000 genomes]
rs4319547	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs4758643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758644	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4758645	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4758646	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4758648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4758662	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4997380	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs55834409	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6488933	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6488939	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6488951	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6488958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489002	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489156	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs6489157	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7135419	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294559	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7301515	0.84[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs7307735	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7314638	0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs7316114	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7398014	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7952868	0.88[EUR][1000 genomes]
rs7953007	0.81[ASN][1000 genomes]
rs7956480	0.94[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs7964138	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7969429	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7973869	0.83[EUR][1000 genomes]
rs7974262	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975747	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs9705654	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs9788145	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9988963	0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4758666	GATC	cis	cerebellum	SCAN
rs4758666	B3GNT4	cis	cerebellum	SCAN
rs4758666	NME2P1	cis	cerebellum	SCAN
rs4758666	GTF2H3	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122860600-122905000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:122863800-122905000	Weak transcription	Dnd41	blood
3	chr12:122884600-122905200	Weak transcription	Colonic Mucosa	Colon
4	chr12:122885200-122904600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:122885200-122905200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:122885200-122905400	Weak transcription	Fetal Thymus	thymus
7	chr12:122885200-122905400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:122885200-122906000	Weak transcription	Ovary	ovary
9	chr12:122885400-122905000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr12:122885600-122905400	Weak transcription	NH-A	brain
11	chr12:122886200-122905400	Weak transcription	Right Ventricle	heart
12	chr12:122887200-122906200	Weak transcription	Lung	lung
13	chr12:122887600-122904800	Weak transcription	HMEC	breast
14	chr12:122888800-122905000	Weak transcription	Esophagus	oesophagus
15	chr12:122889000-122904600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:122889000-122905000	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:122890000-122905000	Weak transcription	Primary T cells from cord blood	blood
18	chr12:122891000-122903000	Weak transcription	Pancreas	Pancrea
19	chr12:122891000-122905200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:122892200-122904000	Weak transcription	HSMMtube	muscle
21	chr12:122892200-122904800	Weak transcription	Brain Angular Gyrus	brain
22	chr12:122892600-122905000	Weak transcription	Fetal Intestine Large	intestine
23	chr12:122895200-122905200	Weak transcription	Fetal Heart	heart
24	chr12:122896000-122903000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:122896200-122904800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:122896200-122905000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr12:122896400-122905600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:122897200-122903200	Weak transcription	Left Ventricle	heart
29	chr12:122897200-122905000	Weak transcription	Spleen	Spleen
30	chr12:122898000-122904800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:122898000-122905000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:122898000-122905400	Weak transcription	Fetal Kidney	kidney
33	chr12:122898200-122905000	Weak transcription	Brain Substantia Nigra	brain
34	chr12:122898200-122905000	Weak transcription	Stomach Mucosa	stomach
35	chr12:122898200-122905000	Weak transcription	NHDF-Ad	bronchial
36	chr12:122898200-122905200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:122898200-122905600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr12:122898400-122903200	Weak transcription	K562	blood
39	chr12:122898400-122904800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:122898600-122904400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:122898600-122904600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr12:122898600-122904600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:122898600-122904800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:122898600-122904800	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:122898600-122905000	Weak transcription	Adipose Nuclei	Adipose
46	chr12:122898600-122905000	Weak transcription	Brain Anterior Caudate	brain
47	chr12:122898600-122905000	Weak transcription	Fetal Brain Female	brain
48	chr12:122898600-122905400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:122898800-122904800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:122898800-122904800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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