Variant report

Variant	rs7964138
Chromosome Location	chr12:122950375-122950376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122883342..122886247-chr12:122947542..122950684,3	MCF-7	breast:
2	chr12:122949994..122952533-chr12:123234424..123237485,3	MCF-7	breast:
3	chr12:122904060..122906537-chr12:122948950..122950891,2	MCF-7	breast:
4	chr12:122947417..122950530-chr12:122951037..122954189,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139726	Chromatin interaction
ENSG00000130779	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10161534	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10734915	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10734918	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10734924	0.81[ASW][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs10744192	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744208	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10744209	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744210	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744211	0.89[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744217	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10744220	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10744242	0.83[ASW][hapmap];0.90[YRI][hapmap]
rs10744287	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10773075	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.86[TSI][hapmap]
rs10773088	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10773103	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10773104	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10773152	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.88[TSI][hapmap]
rs10773167	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773172	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10773176	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773178	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773208	0.81[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10773394	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10846664	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs10846688	0.92[CHB][hapmap]
rs10846699	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846746	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846764	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846792	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846830	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10846920	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846921	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10846931	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10846968	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs10846978	0.81[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10847179	0.81[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10847242	1.00[JPT][hapmap]
rs10998	0.81[ASW][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11057786	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11057797	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11057882	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11058034	0.88[EUR][1000 genomes]
rs11058209	0.82[EUR][1000 genomes]
rs11058226	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11058233	0.82[EUR][1000 genomes]
rs11058251	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11058282	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11058402	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11616082	0.86[EUR][1000 genomes]
rs11836188	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12369858	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs12372756	0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12423420	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12425970	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12581249	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1473553	0.81[ASW][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1803290	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1818050	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1973463	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2062488	0.86[TSI][hapmap]
rs2341439	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28730465	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34129612	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3817011	0.89[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs4319547	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4356269	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs4758643	1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4758644	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4758645	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4758646	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4758648	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4758657	0.95[YRI][hapmap]
rs4758662	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4758666	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]
rs4997380	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs55834409	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6416295	0.83[ASW][hapmap];0.86[YRI][hapmap]
rs6488939	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6488951	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6488958	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6489002	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6489014	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs6489051	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs6489156	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs6489157	0.81[ASW][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7134381	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs7135419	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7294559	0.89[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap]
rs7296680	0.95[YRI][hapmap]
rs7298839	0.91[YRI][hapmap]
rs7301515	0.95[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7307735	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs7311573	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs7314638	0.81[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7316114	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7397990	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs7398014	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7952868	0.82[EUR][1000 genomes]
rs7954006	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs7955513	0.83[ASW][hapmap];0.91[YRI][hapmap]
rs7956480	0.84[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap]
rs7959238	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7963773	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7969429	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974262	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975747	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs9705654	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs9788145	0.86[EUR][1000 genomes]
rs9988963	0.81[ASW][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]

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	nsv973945	chr12:122923254-122958354	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7964138	NME2P1	cis	cerebellum	SCAN
rs7964138	GTF2H3	cis	cerebellum	SCAN
rs7964138	UGT2B17	trans	lymphoblastoid	seeQTL
rs7964138	B3GNT4	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122922800-122960400	Weak transcription	Right Atrium	heart
2	chr12:122938800-122957000	Weak transcription	Thymus	Thymus
3	chr12:122939600-122955200	Weak transcription	Fetal Thymus	thymus
4	chr12:122941200-122957200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:122943600-122951400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:122944400-122957000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:122945800-122956000	Weak transcription	GM12878-XiMat	blood
8	chr12:122947400-122951600	Enhancers	Placenta	Placenta
9	chr12:122948200-122952000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:122948600-122957000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:122948800-122951200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:122948800-122951400	Weak transcription	Esophagus	oesophagus
13	chr12:122948800-122955600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:122948800-122955800	Weak transcription	Fetal Intestine Small	intestine
15	chr12:122948800-122957000	Weak transcription	Fetal Intestine Large	intestine
16	chr12:122948800-122958000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:122948800-122958000	Weak transcription	Psoas Muscle	Psoas
18	chr12:122949000-122955800	Weak transcription	HSMM	muscle
19	chr12:122949200-122951200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:122949200-122955600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:122949200-122955800	Weak transcription	HepG2	liver
22	chr12:122949600-122952600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:122949600-122955600	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:122949600-122955800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:122949600-122957000	Weak transcription	Lung	lung
26	chr12:122949800-122951000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:122949800-122951200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:122949800-122951200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:122949800-122951200	Weak transcription	NHEK	skin
30	chr12:122949800-122951400	Weak transcription	HMEC	breast
31	chr12:122949800-122955600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:122949800-122955600	Weak transcription	A549	lung
33	chr12:122949800-122955600	Weak transcription	NH-A	brain
34	chr12:122949800-122955600	Weak transcription	NHDF-Ad	bronchial
35	chr12:122949800-122955600	Weak transcription	NHLF	lung
36	chr12:122949800-122955800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:122949800-122955800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:122949800-122955800	Weak transcription	Stomach Mucosa	stomach
39	chr12:122949800-122955800	Weak transcription	Osteobl	bone
40	chr12:122949800-122957000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr12:122949800-122957200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:122949800-122957600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:122949800-122958000	Weak transcription	Small Intestine	intestine
44	chr12:122949800-122958200	Weak transcription	Pancreas	Pancrea
45	chr12:122950000-122951200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:122950000-122956000	Weak transcription	Primary monocytes fromperipheralblood	blood

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