Variant report

Variant	rs11130536
Chromosome Location	chr3:56668522-56668523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:56666467-56668756	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56666598..56668908-chr3:56715764..56717337,2	MCF-7	breast:

Variant related genes	Relation type
FAM208A	TF binding region
ENSG00000163946	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10212341	0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1045926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10865999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10866000	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130538	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11706624	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs11714608	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11714897	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11715395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11719656	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11921326	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488218	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12490749	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493637	0.84[ASN][1000 genomes]
rs12636773	0.89[ASN][1000 genomes]
rs12715490	0.89[ASN][1000 genomes]
rs13094666	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13097030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13097288	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1352766	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1491166	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs17056878	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17216740	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2004199	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029464	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029465	0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs2035798	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2046823	0.85[GIH][hapmap]
rs2054987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2054988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2291499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2317133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2317245	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs282533	0.82[CHB][hapmap]
rs35998149	0.86[ASN][1000 genomes]
rs3732512	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4093514	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4681746	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4681951	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4681963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974220	0.89[ASN][1000 genomes]
rs4974224	0.81[EUR][1000 genomes]
rs57800049	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6445805	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6445806	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6445807	0.84[ASN][1000 genomes]
rs66529035	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6774323	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6785479	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6798118	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6799576	0.83[ASN][1000 genomes]
rs6802051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804262	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6805469	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72877266	0.83[ASN][1000 genomes]
rs7432897	0.84[ASN][1000 genomes]
rs7612599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7618024	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs7626378	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7629559	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9811046	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9820759	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9822876	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs9840528	0.94[CEU][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9842283	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9845096	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9845655	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9846282	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9858728	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862490	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9881005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9881154	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9881789	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9881961	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9985253	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9985254	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11130536	C12orf32	trans	parietal	SCAN
rs11130536	C3orf51	cis	cerebellum	SCAN
rs11130536	CCDC66	cis	cerebellum	SCAN
rs11130536	ERC2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:56646600-56669000	Weak transcription	Small Intestine	intestine
9	chr3:56646800-56673600	Weak transcription	Right Ventricle	heart
10	chr3:56647000-56672200	Weak transcription	Gastric	stomach
11	chr3:56647400-56707400	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr3:56647400-56707800	Strong transcription	Fetal Thymus	thymus
13	chr3:56651400-56702000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:56652800-56701400	Weak transcription	Psoas Muscle	Psoas
15	chr3:56656200-56683000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:56657400-56683800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:56657600-56675800	Strong transcription	Fetal Muscle Leg	muscle
18	chr3:56657800-56678000	Weak transcription	Fetal Brain Male	brain
19	chr3:56659000-56673000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:56659400-56676200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:56660600-56670800	Weak transcription	Fetal Brain Female	brain
22	chr3:56661400-56710600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:56661800-56674800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:56662200-56672800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:56662400-56670800	Weak transcription	Brain Anterior Caudate	brain
26	chr3:56662400-56670800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:56662400-56672800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr3:56664000-56670800	Weak transcription	NHDF-Ad	bronchial
29	chr3:56664000-56688000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:56664000-56694800	Weak transcription	Stomach Mucosa	stomach
31	chr3:56664800-56687400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr3:56664800-56711000	Strong transcription	Dnd41	blood
33	chr3:56665000-56669000	Strong transcription	Fetal Intestine Large	intestine
34	chr3:56665000-56671200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:56665000-56687800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:56665000-56690400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr3:56665000-56707800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:56665200-56671600	Strong transcription	Osteobl	bone
39	chr3:56665200-56686600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:56665200-56691800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:56665200-56698800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:56665200-56707200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:56665400-56675200	Weak transcription	Pancreas	Pancrea
44	chr3:56665400-56683200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:56665400-56687000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:56665600-56676200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:56665800-56668800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr3:56665800-56671600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr3:56665800-56687400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:56665800-56687400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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