Variant report

Variant	rs4760332
Chromosome Location	chr12:58222672-58222673
allele	A/C
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	MAFK	chr12:58222601-58222801	HepG2	liver:	n/a	chr12:58222687-58222698

No.	Distal block	Cell Line	Cell type
1	chr12:58217743..58220104-chr12:58222008..58224494,2	MCF-7	breast:
2	chr12:58185279..58187890-chr12:58221486..58223214,2	K562	blood:
3	chr12:58212149..58213696-chr12:58221268..58222897,2	K562	blood:

Variant related genes	Relation type
CTDSP2	TF binding region
MIR26A2	TF binding region
ENSG00000135407	Chromatin interaction
ENSG00000207789	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1021469	0.83[JPT][hapmap]
rs10431552	0.88[JPT][hapmap]
rs10444569	0.82[AMR][1000 genomes]
rs10747783	0.88[JPT][hapmap]
rs10747784	0.81[EUR][1000 genomes]
rs10747786	0.94[JPT][hapmap]
rs10747787	0.94[JPT][hapmap]
rs10783847	0.88[JPT][hapmap]
rs10783848	0.86[JPT][hapmap]
rs10783850	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10783851	0.87[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783853	0.86[ASW][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs10783854	0.87[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10783855	0.88[CEU][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10783856	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10877011	0.85[YRI][hapmap]
rs10877012	0.88[JPT][hapmap]
rs10877013	0.81[JPT][hapmap]
rs10877014	0.88[JPT][hapmap]
rs10877015	0.88[JPT][hapmap]
rs10877016	0.88[JPT][hapmap]
rs10877019	0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs10877022	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877024	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877025	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877026	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10877028	0.88[CEU][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap]
rs10877029	0.94[JPT][hapmap]
rs10877030	0.94[JPT][hapmap]
rs10877031	0.82[AMR][1000 genomes]
rs11172333	0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs11172335	0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs11172343	0.88[JPT][hapmap];1.00[YRI][hapmap]
rs11172344	0.88[JPT][hapmap]
rs11172349	0.84[CHB][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs11172351	0.84[CHB][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11172361	0.81[EUR][1000 genomes]
rs11172362	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11172367	0.94[JPT][hapmap]
rs11172369	0.94[JPT][hapmap];0.85[YRI][hapmap]
rs11172371	0.85[YRI][hapmap]
rs12426201	0.82[AMR][1000 genomes]
rs1599750	0.88[CEU][hapmap];0.90[CHD][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1599751	0.88[CEU][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1599931	0.93[JPT][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes]
rs1875124	0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs1875125	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2002275	0.86[ASW][hapmap];0.87[MEX][hapmap]
rs2069502	0.83[JPT][hapmap];1.00[LWK][hapmap]
rs2072052	0.83[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs3825079	0.84[CHB][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.85[YRI][hapmap]
rs4237844	0.87[ASW][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs4646536	0.88[JPT][hapmap]
rs4760171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760172	0.80[CHD][hapmap];0.94[JPT][hapmap]
rs4760333	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760335	0.82[EUR][1000 genomes]
rs4760339	0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs4760341	0.94[JPT][hapmap]
rs5017863	0.83[AMR][1000 genomes]
rs6581155	0.88[JPT][hapmap]
rs703842	0.88[JPT][hapmap]
rs724834	0.88[JPT][hapmap];0.85[YRI][hapmap]
rs7312623	0.81[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs7489290	1.00[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8181644	0.88[JPT][hapmap]
rs870392	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs871871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs923829	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs4760332	METTL21B	cis	Whole Blood	GTEx
rs4760332	XRCC6BP1	cis	Whole Blood	GTEx
rs4760332	METTL21B	cis	Muscle Skeletal	GTEx
rs4760332	XRCC6BP1	cis	multi-tissue	Pritchard
rs4760332	TSFM	cis	cerebellum	SCAN
rs4760332	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760332	FAM119B	cis	cerebellum	SCAN
rs4760332	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs4760332	TSFM	cis	multi-tissue	Pritchard
rs4760332	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs4760332	CDK2	cis	parietal	SCAN
rs4760332	XRCC6BP1	cis	Artery Tibial	GTEx
rs4760332	FAM119B	cis	Temporal Cortex	GTEx
rs4760332	GPR84	cis	cerebellum	SCAN
rs4760332	PPP1R1A	cis	parietal	SCAN
rs4760332	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs4760332	METTL21B	cis	Esophagus Muscularis	GTEx
rs4760332	DKFZP586D0919	cis	multi-tissue	Pritchard
rs4760332	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4760332	FAM119B	cis	Cerebellum	GTEx
rs4760332	MUCL1	cis	parietal	SCAN
rs4760332	TSPAN31	cis	parietal	SCAN
rs4760332	FAM119B	cis	parietal	SCAN
rs4760332	FAM119B	cis	Frontal Cortex	GTEx
rs4760332	TSFM	cis	lymphoblastoid	seeQTL
rs4760332	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs4760332	FAM119B	cis	Lymphoblastoid	GTEx
rs4760332	FAM119B	cis	lymphoblastoid	seeQTL
rs4760332	XRCC6BP1	cis	lung	GTEx
rs4760332	TSPAN31	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58207800-58222800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:58209400-58226800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:58211200-58223800	Strong transcription	Osteobl	bone
4	chr12:58211400-58224600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:58211400-58224800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:58211600-58222800	Strong transcription	Fetal Stomach	stomach
7	chr12:58211600-58224000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:58212000-58222800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:58212000-58224400	Strong transcription	Fetal Intestine Large	intestine
10	chr12:58212000-58224800	Strong transcription	Thymus	Thymus
11	chr12:58212200-58222800	Strong transcription	Fetal Intestine Small	intestine
12	chr12:58212200-58223600	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:58212200-58223800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:58212200-58224800	Strong transcription	Brain Germinal Matrix	brain
15	chr12:58212400-58222800	Strong transcription	Primary hematopoietic stem cells	blood
16	chr12:58212400-58222800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:58212400-58223600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:58212400-58223600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:58212600-58222800	Strong transcription	Brain Cingulate Gyrus	brain
20	chr12:58212600-58223200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr12:58212600-58224000	Strong transcription	Fetal Lung	lung
22	chr12:58212600-58224200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr12:58213000-58223200	Strong transcription	NHLF	lung
24	chr12:58213000-58223400	Strong transcription	Fetal Brain Female	brain
25	chr12:58213200-58222800	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:58213400-58223000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:58213400-58223000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:58213400-58223000	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr12:58213400-58223200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr12:58213400-58224000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:58213600-58223000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:58213600-58224000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:58213600-58224400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:58213800-58224000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:58214000-58222800	Strong transcription	Brain Hippocampus Middle	brain
36	chr12:58214000-58223000	Strong transcription	Brain Angular Gyrus	brain
37	chr12:58214000-58223800	Strong transcription	Primary B cells from cord blood	blood
38	chr12:58214200-58223000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:58214400-58223000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:58214400-58223200	Strong transcription	Primary T cells from cord blood	blood
41	chr12:58214400-58223200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:58214400-58224000	Strong transcription	Dnd41	blood
43	chr12:58215000-58222800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr12:58215000-58222800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr12:58215000-58223000	Strong transcription	Ovary	ovary
46	chr12:58215000-58223200	Strong transcription	Aorta	Aorta
47	chr12:58215000-58223200	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr12:58215000-58223400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr12:58215000-58223400	Strong transcription	NHDF-Ad	bronchial
50	chr12:58215200-58223400	Strong transcription	H1 Cell Line	embryonic stem cell

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