Variant report

Variant	rs180412
Chromosome Location	chr12:47167078-47167079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11183608	0.85[EUR][1000 genomes]
rs12316767	0.85[EUR][1000 genomes]
rs1468970	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1468971	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1468972	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180403	0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs180405	0.85[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180407	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180408	0.86[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180409	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs180410	0.91[CHB][hapmap];0.83[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180415	0.91[CHB][hapmap];0.83[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180416	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs180417	0.91[CHB][hapmap];0.83[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180419	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180420	0.84[CHB][hapmap];0.82[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180421	0.90[CHB][hapmap];0.82[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180423	0.81[ASN][1000 genomes]
rs180426	0.82[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs180427	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs180429	0.90[CHB][hapmap];0.82[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs180430	0.90[CHB][hapmap];0.82[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2080689	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287471	0.85[EUR][1000 genomes]
rs2408623	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2430916	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2430920	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2430921	0.85[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465582	0.85[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465584	0.85[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465595	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465614	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2543334	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2543335	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2715775	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2715783	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7316285	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv826361	chr12:47159545-47200894	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47157400-47172800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:47161600-47173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:47163400-47167800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr12:47163600-47167400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:47163600-47168400	Enhancers	Hela-S3	cervix
6	chr12:47164200-47187800	Genic enhancers	Liver	Liver
7	chr12:47164600-47167400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:47164600-47167400	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:47164600-47167800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr12:47164600-47168400	Enhancers	NHDF-Ad	bronchial
11	chr12:47164600-47168400	Enhancers	NHLF	lung
12	chr12:47164800-47169600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:47165000-47168000	Weak transcription	Fetal Heart	heart
14	chr12:47165000-47169000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:47165200-47169400	Enhancers	Fetal Muscle Leg	muscle
16	chr12:47165200-47187200	Weak transcription	Fetal Kidney	kidney
17	chr12:47165400-47167600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:47165600-47167600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:47165600-47167800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:47165600-47182000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:47165800-47167400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:47165800-47167400	Weak transcription	NH-A	brain
23	chr12:47165800-47168200	Weak transcription	Left Ventricle	heart
24	chr12:47165800-47169600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:47166000-47167400	Genic enhancers	HSMM	muscle
26	chr12:47166000-47167800	Weak transcription	Adipose Nuclei	Adipose
27	chr12:47166000-47168400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:47166000-47169000	Enhancers	HSMMtube	muscle
29	chr12:47166800-47167200	Genic enhancers	Muscle Satellite Cultured Cells	--
30	chr12:47166800-47167400	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:47166800-47168400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:47166800-47169400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:47167000-47167600	Enhancers	Pancreas	Pancrea
34	chr12:47167000-47167600	Enhancers	Psoas Muscle	Psoas
35	chr12:47167000-47167800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:47167000-47168000	Enhancers	Fetal Brain Male	brain
37	chr12:47167000-47168400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:47167000-47168400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:47167000-47168400	Enhancers	Fetal Lung	lung
40	chr12:47167000-47168400	Enhancers	Osteobl	bone
41	chr12:47167000-47173200	Enhancers	HepG2	liver

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