Variant report

Variant	rs12296766
Chromosome Location	chr12:57684943-57684944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57683981..57686503-chr12:57687593..57689362,2	MCF-7	breast:
2	chr12:57683640..57687551-chr12:57695427..57698739,4	K562	blood:
3	chr12:57677431..57681083-chr12:57683633..57687091,3	K562	blood:

Variant related genes	Relation type
ENSG00000179912	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10747777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747778	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783818	0.80[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783820	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783823	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876976	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[AMR][1000 genomes]
rs10876977	0.82[ASN][1000 genomes]
rs10876978	0.81[AMR][1000 genomes]
rs11172156	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172160	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172165	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172169	0.89[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172177	0.80[EUR][1000 genomes]
rs11172190	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs11609986	0.96[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12310220	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12579911	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs12812140	0.96[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1798710	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs2063778	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2280139	0.80[JPT][hapmap]
rs35032945	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3923885	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4075325	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4760192	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760193	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760228	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4760236	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4760308	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4760348	1.00[CEU][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760356	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760357	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs481196	1.00[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs491750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs512223	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs533975	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs537482	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs543410	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs560048	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs568793	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs575153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs6581131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581134	0.95[CHB][hapmap];0.98[GIH][hapmap];0.84[LWK][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581135	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6581136	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6581139	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7132367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7133366	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7133939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135142	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7298418	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7307059	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7309659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7313824	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7314266	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7358684	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7398058	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7486863	0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7975649	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7977908	1.00[CEU][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12296766	SPRY2	trans	lymphoblastoid	seeQTL
rs12296766	XRCC6BP1	cis	multi-tissue	Pritchard
rs12296766	ZNF385A	cis	parietal	SCAN
rs12296766	OR6C4	cis	parietal	SCAN
rs12296766	APOF	cis	parietal	SCAN
rs12296766	TSPAN31	cis	cerebellum	SCAN
rs12296766	DKFZP586D0919	cis	multi-tissue	Pritchard
rs12296766	SILV	cis	parietal	SCAN
rs12296766	ARHGAP9	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57654800-57705400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:57662800-57706000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr12:57667600-57685600	Weak transcription	Fetal Heart	heart
4	chr12:57667600-57687200	Weak transcription	Psoas Muscle	Psoas
5	chr12:57670400-57707000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr12:57670600-57693000	Strong transcription	Fetal Muscle Leg	muscle
7	chr12:57670600-57694400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:57670600-57698600	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:57670600-57700000	Strong transcription	Fetal Muscle Trunk	muscle
10	chr12:57671000-57694400	Strong transcription	Adipose Nuclei	Adipose
11	chr12:57671000-57700000	Strong transcription	Liver	Liver
12	chr12:57671200-57690400	Strong transcription	Fetal Brain Female	brain
13	chr12:57671600-57692200	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr12:57672200-57688400	Weak transcription	Small Intestine	intestine
15	chr12:57672800-57688400	Weak transcription	Colonic Mucosa	Colon
16	chr12:57674400-57697000	Strong transcription	Placenta	Placenta
17	chr12:57674600-57685000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:57674600-57686800	Weak transcription	Esophagus	oesophagus
19	chr12:57674600-57693200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:57674600-57693600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:57674600-57694200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr12:57674600-57697000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:57674600-57700000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:57674600-57702600	Weak transcription	HUVEC	blood vessel
25	chr12:57674600-57704400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:57674800-57685600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr12:57674800-57688400	Weak transcription	NHDF-Ad	bronchial
28	chr12:57674800-57688800	Weak transcription	HMEC	breast
29	chr12:57674800-57691200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:57674800-57693600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:57674800-57694200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr12:57674800-57697400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:57674800-57697800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:57674800-57700000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:57674800-57701000	Strong transcription	Primary T cells from cord blood	blood
36	chr12:57675000-57690000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr12:57675000-57698400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:57675000-57699400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr12:57675000-57700000	Strong transcription	Fetal Thymus	thymus
40	chr12:57675000-57701000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr12:57675400-57707000	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr12:57675600-57694800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:57676200-57700000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:57676200-57700000	Strong transcription	Fetal Intestine Large	intestine
45	chr12:57677000-57685800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr12:57677200-57687000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr12:57677600-57685600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:57677600-57713000	Weak transcription	Stomach Mucosa	stomach
49	chr12:57677800-57685400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:57677800-57688600	Weak transcription	Hela-S3	cervix

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