Variant report

Variant	rs10774480
Chromosome Location	chr12:1091657-1091658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10744530	0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs10774482	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs10848433	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs10849612	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10849620	0.87[CHB][hapmap];0.81[CHD][hapmap];0.80[GIH][hapmap];0.92[JPT][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs11061620	0.93[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs11064634	0.88[ASN][1000 genomes]
rs11064640	0.80[ASN][1000 genomes]
rs12370704	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12582029	0.83[ASN][1000 genomes]
rs12811563	0.81[ASN][1000 genomes]
rs1362135	0.94[CHB][hapmap];0.92[JPT][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap]
rs2079299	0.83[ASN][1000 genomes]
rs2097859	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs2107650	0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs2887533	0.86[JPT][hapmap]
rs3924361	1.00[YRI][hapmap]
rs4765965	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs4765969	0.81[ASN][1000 genomes]
rs61088399	0.83[ASN][1000 genomes]
rs61917255	0.83[ASN][1000 genomes]
rs7134570	0.86[JPT][hapmap]
rs7311276	0.94[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7956944	0.81[ASN][1000 genomes]
rs7974198	0.81[ASN][1000 genomes]
rs7974686	0.94[CHB][hapmap];0.92[JPT][hapmap];0.80[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	nsv556890	chr12:662448-1100555	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10774480	TPM2	trans	lymphoblastoid	seeQTL
rs10774480	SLC6A13	cis	cerebellum	SCAN
rs10774480	C12orf32	cis	cerebellum	SCAN
rs10774480	ERC1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1068000-1097600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr12:1068000-1098600	Weak transcription	Aorta	Aorta
3	chr12:1072800-1097800	Weak transcription	Pancreas	Pancrea
4	chr12:1073200-1099600	Weak transcription	Gastric	stomach
5	chr12:1074200-1097200	Weak transcription	Fetal Stomach	stomach
6	chr12:1076200-1097600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:1076400-1097600	Weak transcription	Brain Angular Gyrus	brain
8	chr12:1076400-1097600	Weak transcription	Fetal Intestine Small	intestine
9	chr12:1077600-1097600	Weak transcription	Fetal Brain Male	brain
10	chr12:1077800-1097800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr12:1078000-1097200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:1078000-1097600	Weak transcription	Brain Hippocampus Middle	brain
13	chr12:1078000-1097600	Weak transcription	Fetal Brain Female	brain
14	chr12:1078000-1099000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:1078400-1097600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:1079200-1097600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:1081400-1097400	Weak transcription	Fetal Lung	lung
18	chr12:1081600-1097600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:1081600-1097600	Weak transcription	Ovary	ovary
20	chr12:1081600-1099600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:1081800-1095400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:1082600-1099000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:1083800-1097600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:1084400-1097200	Weak transcription	Thymus	Thymus
25	chr12:1084400-1097800	Weak transcription	HSMM	muscle
26	chr12:1085000-1097600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:1085000-1097600	Weak transcription	Hela-S3	cervix
28	chr12:1086600-1094800	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:1086600-1097200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:1086600-1097600	Weak transcription	Brain Anterior Caudate	brain
31	chr12:1086600-1097600	Weak transcription	Left Ventricle	heart
32	chr12:1086600-1097600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:1087600-1097600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:1089000-1097200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:1089600-1097600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:1090400-1097800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:1090600-1091800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:1090600-1091800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:1090600-1097600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:1090800-1097800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:1090800-1097800	Weak transcription	NHEK	skin
42	chr12:1091000-1091800	Enhancers	K562	blood
43	chr12:1091400-1092800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:1091400-1097200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:1091400-1097400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr12:1091400-1097600	Weak transcription	NHDF-Ad	bronchial

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