Variant report

Variant	rs11054731
Chromosome Location	chr12:12376465-12376466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10772536	0.91[EUR][1000 genomes]
rs10772537	0.90[EUR][1000 genomes]
rs10772540	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10845489	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs10845491	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10845492	0.90[EUR][1000 genomes]
rs10845494	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10845495	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10845496	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10845501	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11054718	0.82[EUR][1000 genomes]
rs11054724	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11054744	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11054754	0.83[CEU][hapmap]
rs11609634	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs12366664	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12823243	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1819871	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2284396	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs2302684	0.81[EUR][1000 genomes]
rs2417086	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3782528	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4477532	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs4763785	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61920859	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6488507	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7294695	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7302808	0.82[EUR][1000 genomes]
rs7305037	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7956548	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7956971	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7979447	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Coronary artery calcification	23870195	GWAS catalog

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
2	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
3	chr12:12368200-12379000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:12368200-12381400	Weak transcription	Gastric	stomach
5	chr12:12368200-12384200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:12368600-12381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:12368600-12381400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:12370600-12380800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:12370600-12381000	Weak transcription	Left Ventricle	heart
11	chr12:12370800-12379000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:12370800-12380800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:12370800-12392200	Weak transcription	Brain Substantia Nigra	brain
14	chr12:12371800-12378200	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:12372200-12376800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:12373000-12380800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:12373000-12381200	Weak transcription	Lung	lung
18	chr12:12374000-12377800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:12374200-12376600	Weak transcription	K562	blood
20	chr12:12374600-12377000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr12:12374600-12381000	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:12374600-12381400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr12:12374800-12380600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr12:12374800-12380600	Weak transcription	Brain Angular Gyrus	brain
25	chr12:12374800-12380800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:12374800-12383200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:12375000-12377000	Weak transcription	HSMM	muscle
28	chr12:12375000-12378200	Weak transcription	Fetal Intestine Large	intestine
29	chr12:12375000-12379200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr12:12375000-12380800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:12375200-12379200	Weak transcription	Liver	Liver
32	chr12:12375200-12379400	Weak transcription	Fetal Kidney	kidney
33	chr12:12375400-12376800	Weak transcription	HepG2	liver
34	chr12:12375600-12377200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:12375800-12379000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:12376000-12376800	Enhancers	A549	lung
37	chr12:12376200-12377200	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr12:12376200-12377800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:12376200-12377800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:12376200-12378400	Enhancers	GM12878-XiMat	blood
41	chr12:12376400-12376800	Weak transcription	Brain Anterior Caudate	brain

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