Variant report

Variant	rs7964008
Chromosome Location	chr12:120918397-120918398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120916744..120918980-chr12:120965515..120967797,2	K562	blood:
2	chr12:120916248..120922154-chr12:120930907..120936100,10	MCF-7	breast:
3	chr12:120916702..120919183-chr12:120925970..120929169,3	MCF-7	breast:
4	chr12:120916613..120919534-chr12:120931915..120935906,4	MCF-7	breast:
5	chr12:120906527..120910615-chr12:120916026..120919065,5	K562	blood:

Variant related genes	Relation type
ENSG00000248008	Chromatin interaction
ENSG00000088986	Chromatin interaction
ENSG00000110871	Chromatin interaction
ENSG00000111786	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10789	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11065140	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11548262	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11608807	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11609119	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11611781	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11611814	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11612519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11613214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11614224	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11615264	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11615719	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829765	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16950293	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16950305	1.00[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2280168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35696148	0.83[ASN][1000 genomes]
rs3742049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3759402	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3817301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3829291	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4102203	1.00[CEU][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs4439575	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57646360	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59088579	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59201986	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60162888	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6490292	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66840048	0.86[ASN][1000 genomes]
rs7027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134710	0.97[EUR][1000 genomes]
rs719449	0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs719450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7296473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7297861	0.88[ASN][1000 genomes]
rs7299954	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7314103	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403923	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73403943	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73403947	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73403968	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73403975	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73405628	0.88[ASN][1000 genomes]
rs7957424	0.86[YRI][hapmap]
rs7961895	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7962410	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7973555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7979366	0.92[ASW][hapmap];0.92[YRI][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7964008	POP5	cis	parietal	SCAN
rs7964008	GATC	cis	cerebellum	SCAN
rs7964008	GATC	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120908200-120933200	Weak transcription	Aorta	Aorta
2	chr12:120908400-120919400	Weak transcription	Right Ventricle	heart
3	chr12:120908400-120919800	Weak transcription	Fetal Intestine Large	intestine
4	chr12:120908400-120925800	Weak transcription	Fetal Intestine Small	intestine
5	chr12:120908400-120926000	Weak transcription	HSMMtube	muscle
6	chr12:120908400-120928800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:120908400-120929000	Weak transcription	Psoas Muscle	Psoas
8	chr12:120908400-120932400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:120908400-120932400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:120908600-120925400	Weak transcription	Pancreas	Pancrea
11	chr12:120908600-120927200	Weak transcription	Fetal Brain Female	brain
12	chr12:120908600-120928200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:120908600-120928600	Weak transcription	Spleen	Spleen
14	chr12:120908600-120928800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:120908600-120932800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:120908600-120932800	Weak transcription	Adipose Nuclei	Adipose
17	chr12:120908600-120932800	Weak transcription	Brain Germinal Matrix	brain
18	chr12:120908600-120932800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:120908600-120933000	Weak transcription	Thymus	Thymus
20	chr12:120908800-120926000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr12:120908800-120928400	Weak transcription	Primary T cells from cord blood	blood
22	chr12:120909200-120919400	Weak transcription	Fetal Stomach	stomach
23	chr12:120909200-120919600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:120911000-120932800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:120912000-120928600	Weak transcription	Esophagus	oesophagus
26	chr12:120912600-120929200	Weak transcription	Fetal Thymus	thymus
27	chr12:120912800-120926000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:120912800-120928800	Weak transcription	Placenta	Placenta
29	chr12:120912800-120932600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr12:120913000-120919400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:120913000-120919400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:120913000-120927800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:120913000-120928600	Weak transcription	NHDF-Ad	bronchial
34	chr12:120913000-120932600	Weak transcription	NH-A	brain
35	chr12:120913200-120919400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:120913200-120919800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:120913200-120920600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:120913200-120927000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:120913200-120928400	Weak transcription	NHEK	skin
40	chr12:120913200-120932800	Weak transcription	HSMM	muscle
41	chr12:120913400-120919000	Weak transcription	A549	lung
42	chr12:120913600-120926400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:120913600-120926800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:120913800-120932400	Weak transcription	HMEC	breast
45	chr12:120914000-120920000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:120914400-120919600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:120914400-120921200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:120914400-120932600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr12:120916400-120920800	Enhancers	Primary T cells fromperipheralblood	blood
50	chr12:120916400-120932800	Weak transcription	Liver	Liver

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