Variant report

Variant	rs12310220
Chromosome Location	chr12:57684978-57684979
allele	C/T
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: 5 )

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

rs_ID	r²[population]
rs10747777	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747778	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783818	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783819	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783820	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783823	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876976	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs10876977	0.81[ASN][1000 genomes]
rs10876978	0.82[AMR][1000 genomes]
rs11172156	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172160	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172165	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172169	0.85[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11172170	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172177	0.80[EUR][1000 genomes]
rs11172190	0.88[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs11609986	1.00[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12296766	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	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12812140	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1798710	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap]
rs2063778	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs2280139	0.80[JPT][hapmap]
rs35032945	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3923885	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4075325	0.80[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760192	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760193	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760228	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4760236	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];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4760308	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4760348	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4760356	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760357	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs481196	0.96[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs491750	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs512223	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs533975	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs537482	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs543410	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap]
rs560048	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap]
rs568793	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs575153	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap]
rs6581131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6581134	0.93[ASW][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.96[LWK][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581135	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6581136	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6581139	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7132367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7133366	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7133939	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7135142	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7298418	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7307059	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];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7309659	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7313824	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7314266	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7358684	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7398058	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7486863	0.92[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7975649	0.86[ASN][1000 genomes]
rs7977908	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12310220	TSPAN31	cis	cerebellum	SCAN
rs12310220	APOF	cis	parietal	SCAN
rs12310220	ARHGAP9	cis	cerebellum	SCAN
rs12310220	SILV	cis	parietal	SCAN
rs12310220	OR6C4	cis	parietal	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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