Variant report

Variant	rs9634246
Chromosome Location	chr12:57034388-57034389
allele	A/G
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	chr12:57034142-57034495	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:57034180-57035112	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr12:57034209-57034468	K562	blood:	n/a	n/a
4	POLR2A	chr12:57032764-57034619	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57033589..57036096-chr12:57478215..57479936,2	MCF-7	breast:
2	chr12:57027023..57035553-chr12:57079936..57085201,18	MCF-7	breast:
3	chr12:57028651..57034442-chr12:57080412..57084452,17	K562	blood:

Variant related genes	Relation type
ATP5B	TF binding region
BAZ2A	TF binding region
ENSG00000110958	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1020848	1.00[ASN][1000 genomes]
rs1026565	0.87[CHB][hapmap]
rs10450	0.80[CHB][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap]
rs10459247	0.81[CEU][hapmap]
rs10747769	0.94[ASN][1000 genomes]
rs10783794	0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10876913	0.97[ASN][1000 genomes]
rs10876914	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876915	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1107479	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11171914	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11171916	1.00[ASN][1000 genomes]
rs11171917	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171951	0.93[CHB][hapmap];0.81[JPT][hapmap]
rs11171986	0.82[MEX][hapmap]
rs11835120	1.00[ASN][1000 genomes]
rs11837319	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1465081	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466382	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs1563896	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1563897	0.86[ASN][1000 genomes]
rs1962963	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1979325	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[YRI][hapmap]
rs2035081	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs2255074	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2256341	0.83[EUR][1000 genomes]
rs2290893	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2290894	0.93[CHB][hapmap]
rs2926740	1.00[ASN][1000 genomes]
rs2926741	0.93[CHB][hapmap]
rs2926743	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap]
rs2950387	0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2950388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950389	0.90[JPT][hapmap]
rs2950390	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2950393	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2950394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958123	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2958124	0.95[ASN][1000 genomes]
rs2958127	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2958130	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs2958139	0.92[GIH][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2958145	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2958146	1.00[ASN][1000 genomes]
rs2958149	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[GIH][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs2958153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2958154	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2958155	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3214051	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs36012661	1.00[ASN][1000 genomes]
rs4759028	0.91[ASN][1000 genomes]
rs4759254	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs67046307	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297289	0.92[ASN][1000 genomes]
rs7303216	0.92[ASN][1000 genomes]
rs7313074	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap]
rs7315472	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73337030	1.00[ASN][1000 genomes]
rs7967600	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs7972420	0.95[ASN][1000 genomes]
rs7973157	1.00[ASN][1000 genomes]
rs7975783	0.94[ASN][1000 genomes]
rs7978685	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs7980317	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs7980378	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7980835	0.96[ASN][1000 genomes]
rs898609	0.93[CHB][hapmap]
rs898611	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs9368	0.81[CHB][hapmap]
rs941207	0.93[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941209	0.84[JPT][hapmap]
rs9634247	0.97[ASN][1000 genomes]
rs9634277	0.97[ASN][1000 genomes]
rs9989034	0.99[ASN][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9634246	PRIM1	cis	parietal	SCAN
rs9634246	CELA1	cis	cerebellum	SCAN
rs9634246	KRT1	cis	cerebellum	SCAN
rs9634246	HSD17B6	cis	cerebellum	SCAN
rs9634246	ERBB3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57030400-57038600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:57030600-57035400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:57030600-57036800	Weak transcription	Right Atrium	heart
4	chr12:57030800-57037200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:57031000-57034600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
6	chr12:57031200-57034400	Genic enhancers	Fetal Heart	heart
7	chr12:57031200-57034600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr12:57031200-57035600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:57031200-57036400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:57031400-57034600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:57031400-57035200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:57031400-57035200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr12:57031400-57036200	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:57031400-57037200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr12:57031400-57037200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr12:57031400-57037200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:57031400-57037200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:57031400-57037200	Strong transcription	Thymus	Thymus
19	chr12:57031400-57037200	Strong transcription	NH-A	brain
20	chr12:57031400-57037400	Strong transcription	Brain Germinal Matrix	brain
21	chr12:57031400-57037600	Strong transcription	HSMM	muscle
22	chr12:57031400-57037600	Strong transcription	Osteobl	bone
23	chr12:57031400-57038200	Strong transcription	HSMMtube	muscle
24	chr12:57031400-57038400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:57031400-57038400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:57031400-57038400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:57031600-57034400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:57031600-57034400	Strong transcription	Fetal Kidney	kidney
29	chr12:57031600-57035400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:57031600-57035400	Strong transcription	Left Ventricle	heart
31	chr12:57031600-57036000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:57031600-57036000	Strong transcription	Esophagus	oesophagus
33	chr12:57031600-57036400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:57031600-57036400	Strong transcription	Dnd41	blood
35	chr12:57031600-57036400	Strong transcription	HUVEC	blood vessel
36	chr12:57031600-57036600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr12:57031600-57037200	Strong transcription	Primary T cells from cord blood	blood
38	chr12:57031600-57037200	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr12:57031600-57037200	Strong transcription	Brain Anterior Caudate	brain
40	chr12:57031600-57037200	Strong transcription	Brain Hippocampus Middle	brain
41	chr12:57031600-57037200	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr12:57031600-57037200	Strong transcription	Colonic Mucosa	Colon
43	chr12:57031600-57037200	Strong transcription	Fetal Brain Female	brain
44	chr12:57031600-57037400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:57031600-57037400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:57031600-57037600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:57031600-57037600	Strong transcription	Fetal Lung	lung
48	chr12:57031600-57037800	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr12:57031600-57037800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:57031600-57038000	Strong transcription	Fetal Muscle Trunk	muscle

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