Variant report

Variant	rs10878386
Chromosome Location	chr12:40725928-40725929
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10459264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10784485	0.85[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10784497	0.85[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10878299	0.85[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10878302	0.85[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10878336	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10878452	0.87[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs11175793	0.85[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11175852	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11175902	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11175913	0.85[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11175941	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11175959	0.82[CEU][hapmap];0.86[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11175963	0.85[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11175964	0.85[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11176022	0.82[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11176052	0.93[JPT][hapmap]
rs11176053	0.93[JPT][hapmap]
rs11176195	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs11176261	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs11564183	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11835105	0.80[CHD][hapmap];0.93[JPT][hapmap]
rs11836288	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12314692	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12316801	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12426498	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes]
rs12426513	0.83[AMR][1000 genomes]
rs12426891	0.85[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1388598	0.89[GIH][hapmap]
rs1491943	0.90[GIH][hapmap]
rs17490817	0.85[EUR][1000 genomes]
rs17490865	0.85[AMR][1000 genomes]
rs17492159	1.00[CEU][hapmap]
rs28365224	0.85[CEU][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28365238	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs3747891	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4318033	0.85[CEU][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56325408	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7133914	0.90[GIH][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7308720	0.85[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs73101520	0.83[AMR][1000 genomes]
rs73108329	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73108368	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv832377	chr12:40704881-40855223	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40640600-40727400	Weak transcription	Spleen	Spleen
2	chr12:40640600-40768200	Weak transcription	Pancreas	Pancrea
3	chr12:40656800-40746400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:40674400-40760400	Weak transcription	Lung	lung
5	chr12:40681200-40763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:40687200-40765000	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr12:40712000-40736600	Weak transcription	Left Ventricle	heart
8	chr12:40712000-40743400	Weak transcription	Aorta	Aorta
9	chr12:40714200-40759200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:40716800-40761600	Weak transcription	Fetal Kidney	kidney
11	chr12:40719600-40735200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:40721000-40734000	Weak transcription	Esophagus	oesophagus
13	chr12:40721600-40726000	Strong transcription	Stomach Smooth Muscle	stomach
14	chr12:40722400-40726200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr12:40722400-40730800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:40722400-40736200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:40722600-40728600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:40722600-40730200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:40722800-40755800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:40724000-40731600	Weak transcription	Brain Angular Gyrus	brain
21	chr12:40724200-40729600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:40724200-40731400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:40724600-40745400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr12:40724800-40728600	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:40724800-40729600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:40724800-40751000	Weak transcription	Brain Anterior Caudate	brain
27	chr12:40725000-40726000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr12:40725000-40726000	Strong transcription	Ovary	ovary
29	chr12:40725000-40730000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:40725000-40736200	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:40725000-40739200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr12:40725200-40727000	Weak transcription	Adipose Nuclei	Adipose
33	chr12:40725200-40732200	Strong transcription	Liver	Liver
34	chr12:40725200-40733200	Strong transcription	Primary B cells from cord blood	blood
35	chr12:40725200-40761200	Weak transcription	Psoas Muscle	Psoas
36	chr12:40725400-40731200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:40725600-40726000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:40725600-40726200	Strong transcription	A549	lung
39	chr12:40725600-40726600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:40725600-40728600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:40725800-40726000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:40725800-40726200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:40725800-40726200	Enhancers	HMEC	breast

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