Variant report

Variant	rs10774482
Chromosome Location	chr12:1101264-1101265
allele	C/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	CHD1	chr12:1101194-1101477	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:1098467-1101358	MCF10A-Er-Src	breast:	n/a	n/a
3	MXI1	chr12:1098625-1101473	IMR90	lung:	n/a	n/a
4	MXI1	chr12:1100901-1101365	Hela-S3	cervix:	n/a	n/a
5	HCFC1	chr12:1098652-1101574	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:1099408-1101350	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr12:1098938-1101511	Hela-S3	cervix:	n/a	n/a
8	RFX5	chr12:1100854-1101449	Hela-S3	cervix:	n/a	n/a
9	SMARCB1	chr12:1099521-1101321	Hela-S3	cervix:	n/a	n/a
10	ZBTB7A	chr12:1099469-1101372	ECC-1	luminal epithelium:	n/a	chr12:1100728-1100739
11	CTCF	chr12:1101180-1101330	AG10803	skin:	n/a	n/a
12	SIN3A	chr12:1099514-1101397	H1-hESC	embryonic stem cell:	n/a	chr12:1100729-1100740 chr12:1100643-1100651 chr12:1099873-1099884
13	MXI1	chr12:1098181-1102272	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr12:1098283-1102022	MCF10A-Er-Src	breast:	n/a	n/a
15	CHD1	chr12:1098198-1102295	IMR90	lung:	n/a	chr12:1100770-1100780 chr12:1100805-1100815
16	MYC	chr12:1101262-1101894	MCF10A-Er-Src	breast:	n/a	n/a
17	MAX	chr12:1098926-1101522	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:1057369..1058961-chr12:1099742..1102215,2	K562	blood:
2	chr12:1099319..1102192-chr19:46282612..46285259,2	MCF-7	breast:
3	chr1:28974934..28975528-chr12:1100894..1101513,2	Hela-S3	cervix:
4	chr12:1056985..1060702-chr12:1098122..1101434,9	MCF-7	breast:
5	chr12:1097166..1102781-chr12:1103327..1109862,10	MCF-7	breast:

Variant related genes	Relation type
RAD52	TF binding region
ENSG00000250132	TF binding region
ENSG00000002016	Chromatin interaction
ENSG00000104936	Chromatin interaction
ENSG00000082805	Chromatin interaction
ENSG00000270103	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10744530	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs10774480	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10848433	0.88[CHB][hapmap]
rs10849612	0.88[ASN][1000 genomes]
rs10849620	0.82[CHB][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs11061620	0.80[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs11064634	0.88[ASN][1000 genomes]
rs11064640	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12370704	0.88[ASN][1000 genomes]
rs12582029	0.89[ASN][1000 genomes]
rs1362135	0.88[CHB][hapmap];0.80[CHD][hapmap];0.87[MEX][hapmap]
rs2079299	0.85[ASN][1000 genomes]
rs2097859	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs2107650	0.88[CHB][hapmap]
rs4765965	0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs4765969	0.83[ASN][1000 genomes]
rs61088399	0.93[ASN][1000 genomes]
rs61917255	0.93[ASN][1000 genomes]
rs61918692	0.91[ASN][1000 genomes]
rs61918705	0.88[ASN][1000 genomes]
rs6489255	0.81[ASN][1000 genomes]
rs7311276	0.88[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs7956944	0.83[ASN][1000 genomes]
rs7974198	0.83[ASN][1000 genomes]
rs7974686	0.96[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:29 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049944	chr12:282465-1232077	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv541306	chr12:282465-1232077	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv949469	chr12:380411-1122450	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv556892	chr12:673515-1210884	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv898576	chr12:813411-1553450	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv948760	chr12:863833-1542875	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv1052589	chr12:910460-1421493	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	nsv468960	chr12:975276-1455106	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv556941	chr12:975276-1455106	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv1044329	chr12:985144-1403020	Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv541340	chr12:985144-1403020	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
14	nsv470256	chr12:998365-1438761	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv492321	chr12:1011692-1388512	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv898579	chr12:1013176-1510505	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
17	nsv898580	chr12:1024688-1569097	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
18	nsv1036488	chr12:1041097-1445923	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
19	nsv1037825	chr12:1045734-1432940	Bivalent/Poised TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
20	nsv541342	chr12:1045734-1432940	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	nsv868854	chr12:1045935-1354083	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
22	nsv468962	chr12:1047531-1119958	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
23	nsv556942	chr12:1047531-1119958	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
24	esv2762958	chr12:1049279-1554962	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
25	nsv1052559	chr12:1077964-1588543	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
26	nsv898581	chr12:1084783-1527359	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
27	nsv1041799	chr12:1091294-1304839	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
28	nsv541343	chr12:1091294-1304839	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
29	esv3357464	chr12:1099316-1101864	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10774482	ERC1	cis	brain	BrainEAC

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1098600-1101600	Active TSS	Aorta	Aorta
2	chr12:1098600-1101800	Active TSS	Fetal Brain Male	brain
3	chr12:1098800-1101400	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr12:1098800-1101600	Active TSS	Left Ventricle	heart
5	chr12:1098800-1101600	Active TSS	Right Ventricle	heart
6	chr12:1098800-1101800	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr12:1099000-1101600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr12:1099000-1101600	Active TSS	Fetal Muscle Trunk	muscle
9	chr12:1099000-1101800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:1099000-1101800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:1099200-1101400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:1099200-1101400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:1099200-1101400	Active TSS	Colon Smooth Muscle	Colon
14	chr12:1099200-1101400	Active TSS	Fetal Intestine Large	intestine
15	chr12:1099200-1101600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:1099200-1101600	Active TSS	Thymus	Thymus
17	chr12:1099200-1101800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr12:1099200-1101800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:1099200-1101800	Active TSS	Fetal Kidney	kidney
20	chr12:1099200-1102000	Active TSS	Brain Angular Gyrus	brain
21	chr12:1099200-1102000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:1099400-1101400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:1099400-1101400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:1099400-1101400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:1099400-1101400	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr12:1099400-1101400	Active TSS	Fetal Heart	heart
27	chr12:1099400-1101400	Active TSS	Pancreas	Pancrea
28	chr12:1099400-1101400	Active TSS	Rectal Smooth Muscle	rectum
29	chr12:1099400-1101400	Active TSS	A549	lung
30	chr12:1099400-1101400	Active TSS	NHDF-Ad	bronchial
31	chr12:1099400-1101600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr12:1099400-1101600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr12:1099400-1101600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:1099400-1101600	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr12:1099400-1101600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:1099400-1101600	Active TSS	HSMMtube	muscle
37	chr12:1099400-1101800	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr12:1099400-1101800	Active TSS	NHLF	lung
39	chr12:1099400-1102000	Active TSS	H1 Cell Line	embryonic stem cell
40	chr12:1099400-1102000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:1099400-1102000	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr12:1099400-1102200	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr12:1099600-1101600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:1099600-1101600	Active TSS	NHEK	skin
45	chr12:1099600-1101800	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr12:1099800-1101600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:1099800-1102200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:1100000-1101600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:1100200-1101800	Active TSS	HMEC	breast
50	chr12:1100200-1102000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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