Variant report

Variant	rs1962047
Chromosome Location	chr12:58292707-58292708
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	RUNX3	chr12:58292084-58293685	GM12878	blood:	n/a	chr12:58293361-58293370 chr12:58293361-58293370
2	SP1	chr12:58292653-58293452	GM12878	blood:	n/a	n/a
3	STAT3	chr12:58292296-58293686	GM12878	blood:	n/a	chr12:58293210-58293218 chr12:58292527-58292534 chr12:58292794-58292801 chr12:58293174-58293186
4	FOS	chr12:58292318-58293145	MCF10A-Er-Src	breast:	n/a	chr12:58292952-58292963 chr12:58292551-58292560 chr12:58292871-58292879
5	POU2F2	chr12:58292701-58293389	GM12891	blood:	n/a	n/a
6	GATA3	chr12:58292583-58293728	SK-N-SH	brain:	n/a	chr12:58292989-58292999
7	FOXM1	chr12:58292337-58293623	GM12878	blood:	n/a	n/a
8	FOXM1	chr12:58292116-58293576	GM12878	blood:	n/a	n/a
9	RUNX3	chr12:58292172-58293609	GM12878	blood:	n/a	chr12:58293361-58293370 chr12:58293361-58293370
10	SMC3	chr12:58292281-58293416	GM12878	blood:	n/a	n/a
11	MAZ	chr12:58292520-58293570	GM12878	blood:	n/a	chr12:58292726-58292737
12	ATF2	chr12:58292429-58293473	GM12878	blood:	n/a	n/a
13	RELA	chr12:58292076-58293432	GM15510	blood:	n/a	chr12:58292929-58292938 chr12:58292929-58292938
14	RELA	chr12:58292146-58293659	GM19193	blood:	n/a	chr12:58292929-58292938 chr12:58292929-58292938
15	MTA3	chr12:58292006-58293510	GM12878	blood:	n/a	n/a
16	MAZ	chr12:58292633-58293511	IMR90	lung:	n/a	chr12:58292726-58292737
17	NFIC	chr12:58292026-58293669	GM12878	blood:	n/a	n/a
18	TBL1XR1	chr12:58292095-58293635	GM12878	blood:	n/a	n/a
19	BATF	chr12:58292706-58293069	GM12878	blood:	n/a	chr12:58292868-58292878
20	ATF2	chr12:58292128-58293615	GM12878	blood:	n/a	n/a
21	ELF1	chr12:58292683-58293270	GM12878	blood:	n/a	n/a
22	RELA	chr12:58292115-58293516	GM12892	blood:	n/a	chr12:58292929-58292938 chr12:58292929-58292938
23	IRF4	chr12:58292631-58293477	GM12878	blood:	n/a	n/a
24	MXI1	chr12:58292285-58293420	GM12878	blood:	n/a	n/a
25	STAT5A	chr12:58292337-58293481	GM12878	blood:	n/a	chr12:58293210-58293218 chr12:58292527-58292534 chr12:58292794-58292801 chr12:58293174-58293186
26	NFIC	chr12:58292085-58293522	GM12878	blood:	n/a	n/a
27	FOS	chr12:58292692-58293209	MCF10A-Er-Src	breast:	n/a	chr12:58292952-58292963 chr12:58293139-58293146 chr12:58292871-58292879
28	TCF12	chr12:58292583-58293544	SK-N-SH	brain:	n/a	n/a
29	NFATC1	chr12:58292412-58293539	GM12878	blood:	n/a	n/a
30	MTA3	chr12:58291922-58293581	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:58292684-58293452	GM12892	blood:	n/a	n/a
32	SP1	chr12:58292663-58293445	GM12878	blood:	n/a	n/a
33	EP300	chr12:58292174-58293503	GM12878	blood:	n/a	chr12:58292987-58293001 chr12:58293306-58293315
34	BHLHE40	chr12:58292259-58293717	GM12878	blood:	n/a	n/a
35	TBP	chr12:58292530-58293740	GM12878	blood:	n/a	n/a
36	EBF1	chr12:58292372-58293684	GM12878	blood:	n/a	n/a
37	EP300	chr12:58292224-58293558	GM12878	blood:	n/a	chr12:58292987-58293001 chr12:58293306-58293315
38	PAX5	chr12:58292584-58293449	GM12878	blood:	n/a	n/a
39	RELA	chr12:58292068-58293572	GM12878	blood:	n/a	chr12:58292929-58292938 chr12:58292929-58292938
40	MEF2C	chr12:58292432-58293406	GM12878	blood:	n/a	chr12:58292784-58292798 chr12:58293328-58293339 chr12:58292552-58292560
41	PML	chr12:58292707-58293551	GM12878	blood:	n/a	n/a
42	MEF2A	chr12:58292262-58293478	GM12878	blood:	n/a	chr12:58292784-58292798 chr12:58293328-58293339 chr12:58292552-58292560
43	POU2F2	chr12:58292707-58293343	GM12891	blood:	n/a	n/a
44	FOS	chr12:58292450-58293205	MCF10A-Er-Src	breast:	n/a	chr12:58292952-58292963 chr12:58293139-58293146 chr12:58292551-58292560 chr12:58292871-58292879
45	STAT5A	chr12:58291959-58293499	GM12878	blood:	n/a	chr12:58293210-58293218 chr12:58292527-58292534 chr12:58292794-58292801 chr12:58293174-58293186
46	EBF1	chr12:58292677-58293452	GM12878	blood:	n/a	n/a
47	POU2F2	chr12:58292626-58293465	GM12878	blood:	n/a	n/a
48	PML	chr12:58292336-58293599	GM12878	blood:	n/a	n/a
49	RELA	chr12:58292130-58293483	GM10847	blood:	n/a	chr12:58292929-58292938 chr12:58292929-58292938
50	IKZF1	chr12:58292234-58293525	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:58238331..58240066-chr12:58291999..58293854,2	K562	blood:
2	chr12:58290453..58292772-chr12:58301540..58304170,2	K562	blood:
3	chr12:58143079..58147361-chr12:58290608..58293518,3	K562	blood:
4	chr12:58265896..58267925-chr12:58291113..58293138,2	K562	blood:
5	chr12:58236711..58242486-chr12:58286970..58293951,15	MCF-7	breast:
6	chr12:58257328..58259688-chr12:58290813..58293614,3	MCF-7	breast:
7	chr12:58289871..58291670-chr12:58291918..58293741,2	K562	blood:

Variant related genes	Relation type
ENSG00000245651	TF binding region
ENSG00000135446	Chromatin interaction
ENSG00000245651	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10444569	0.83[ASN][1000 genomes]
rs10747786	0.82[CHB][hapmap];0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs10747787	0.82[CHB][hapmap];0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs10783855	0.80[CHD][hapmap]
rs10877028	0.80[CHD][hapmap]
rs10877029	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs10877030	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs10877031	0.83[ASN][1000 genomes]
rs10877032	0.83[ASN][1000 genomes]
rs10877033	0.82[ASN][1000 genomes]
rs10877034	0.80[ASN][1000 genomes]
rs11172367	0.90[CHD][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs11172368	0.83[ASN][1000 genomes]
rs11172369	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs11172371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11172372	0.88[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs11172375	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172378	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12319233	0.83[ASN][1000 genomes]
rs12426201	0.83[ASN][1000 genomes]
rs1599750	0.80[CHD][hapmap]
rs1599931	0.82[CHB][hapmap];0.83[ASN][1000 genomes]
rs2002275	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3751330	0.83[ASN][1000 genomes]
rs3751331	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128707	0.83[ASN][1000 genomes]
rs4237844	0.82[CHB][hapmap];0.90[CHD][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs4237845	0.88[CHB][hapmap];1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs4628718	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4630335	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760172	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs4760339	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs4760340	0.90[CHD][hapmap]
rs4760341	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs59401446	0.80[ASN][1000 genomes]
rs61935769	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581157	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6650217	0.83[ASN][1000 genomes]
rs6650218	0.83[ASN][1000 genomes]
rs6650219	0.83[ASN][1000 genomes]
rs7134797	0.81[ASN][1000 genomes]
rs7306124	0.83[EUR][1000 genomes]
rs7312623	0.82[CHB][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs7954591	0.83[ASN][1000 genomes]
rs7954957	0.88[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs7963992	0.82[ASN][1000 genomes]
rs7969844	0.81[ASN][1000 genomes]
rs7971877	0.88[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs9645819	0.81[ASN][1000 genomes]

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:20)

SNP	Gene	Cis/trans	Tissue	Source
rs1962047	XRCC6BP1	cis	Artery Aorta	GTEx
rs1962047	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs1962047	FAM119B	cis	Lymphoblastoid	GTEx
rs1962047	XRCC6BP1	cis	Whole Blood	GTEx
rs1962047	XRCC6BP1	cis	lung	GTEx
rs1962047	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs1962047	XRCC6BP1	cis	Nerve Tibial	GTEx
rs1962047	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs1962047	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs1962047	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs1962047	STAT6	cis	parietal	SCAN
rs1962047	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs1962047	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs1962047	XRCC6BP1	cis	normal skin	skin_eQTL
rs1962047	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs1962047	FAM119B	cis	cerebellum	SCAN
rs1962047	XRCC6BP1	cis	Esophagus Mucosa	GTEx
rs1962047	XRCC6BP1	cis	Artery Tibial	GTEx
rs1962047	FAM119B	cis	lymphoblastoid	seeQTL
rs1962047	XRCC6BP1	cis	Thyroid	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58288200-58293200	Enhancers	Spleen	Spleen
2	chr12:58289200-58293400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr12:58290200-58293800	Flanking Active TSS	GM12878-XiMat	blood
4	chr12:58290600-58293000	Weak transcription	Gastric	stomach
5	chr12:58290600-58293800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr12:58290600-58293800	Enhancers	HMEC	breast
7	chr12:58290800-58293400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:58290800-58293800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:58290800-58294200	Enhancers	Primary B cells from cord blood	blood
10	chr12:58290800-58294200	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:58290800-58294200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:58291000-58293000	Enhancers	HSMMtube	muscle
13	chr12:58291000-58293200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:58291000-58293200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:58291000-58293200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:58291000-58293200	Enhancers	Fetal Muscle Trunk	muscle
17	chr12:58291000-58293200	Enhancers	Lung	lung
18	chr12:58291000-58293200	Enhancers	Psoas Muscle	Psoas
19	chr12:58291000-58293200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr12:58291000-58293200	Enhancers	HSMM	muscle
21	chr12:58291000-58293400	Enhancers	Aorta	Aorta
22	chr12:58291000-58293400	Enhancers	Esophagus	oesophagus
23	chr12:58291000-58293400	Enhancers	Left Ventricle	heart
24	chr12:58291000-58293400	Enhancers	K562	blood
25	chr12:58291000-58294000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:58291000-58294000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr12:58291000-58294000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr12:58291000-58294200	Enhancers	Fetal Thymus	thymus
29	chr12:58291000-58294400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:58291000-58294400	Enhancers	Primary T cells fromperipheralblood	blood
31	chr12:58291200-58292800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
32	chr12:58291200-58292800	Enhancers	NHEK	skin
33	chr12:58291200-58293000	Enhancers	Fetal Intestine Small	intestine
34	chr12:58291200-58293000	Enhancers	Stomach Mucosa	stomach
35	chr12:58291200-58293200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:58291200-58293200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr12:58291200-58293200	Enhancers	Fetal Muscle Leg	muscle
38	chr12:58291200-58293200	Enhancers	Placenta	Placenta
39	chr12:58291200-58293200	Enhancers	Ovary	ovary
40	chr12:58291200-58293200	Enhancers	Right Atrium	heart
41	chr12:58291200-58293200	Enhancers	Right Ventricle	heart
42	chr12:58291200-58293400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:58291200-58293400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr12:58291200-58293400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:58291200-58293400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:58291200-58293400	Enhancers	Fetal Stomach	stomach
47	chr12:58291200-58293400	Enhancers	HUVEC	blood vessel
48	chr12:58291200-58293400	Enhancers	NHLF	lung
49	chr12:58291200-58293400	Enhancers	Osteobl	bone
50	chr12:58291200-58293800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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