Variant report

Variant	rs3799596
Chromosome Location	chr6:167010458-167010459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12528284	0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12661452	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2032544	0.89[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2032545	0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34324183	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35574615	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35798186	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3778379	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3778380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778381	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3778383	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3799578	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3799579	0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3799581	0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3799582	0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3799589	0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3799590	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799591	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799592	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799593	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3799594	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3799595	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3799599	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3799601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3823196	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823197	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823198	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs3823204	0.82[JPT][hapmap]
rs6907098	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6907443	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs733591	0.81[ASN][1000 genomes]
rs763193	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs9295356	0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9347138	0.90[CHB][hapmap];0.83[EUR][1000 genomes]
rs9348149	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9355586	0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9356491	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9356493	0.90[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9356494	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9366031	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366033	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs960145	0.89[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1029530	chr6:166977678-167016052	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166989000-167011400	Weak transcription	Ovary	ovary
2	chr6:166998000-167011200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr6:167002600-167011400	Weak transcription	Right Atrium	heart
4	chr6:167002600-167013200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:167003000-167010800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr6:167003200-167011200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr6:167003200-167011200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:167003600-167011600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:167003600-167013000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:167004000-167010600	Weak transcription	Fetal Stomach	stomach
11	chr6:167004000-167010600	Weak transcription	Gastric	stomach
12	chr6:167004200-167010800	Weak transcription	Spleen	Spleen
13	chr6:167004200-167012200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:167004600-167010800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:167004800-167010600	Weak transcription	Esophagus	oesophagus
16	chr6:167005400-167010800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:167006000-167012400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:167006200-167011400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:167006600-167011600	Weak transcription	Aorta	Aorta
20	chr6:167008000-167012600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:167008200-167010600	Enhancers	NHLF	lung
22	chr6:167008200-167013000	Enhancers	HSMM	muscle
23	chr6:167008200-167013000	Enhancers	NHDF-Ad	bronchial
24	chr6:167008800-167010600	Weak transcription	Left Ventricle	heart
25	chr6:167008800-167013800	Enhancers	Right Ventricle	heart
26	chr6:167009000-167010600	Enhancers	Brain Hippocampus Middle	brain
27	chr6:167009200-167010600	Enhancers	Brain Cingulate Gyrus	brain
28	chr6:167009200-167010800	Weak transcription	Small Intestine	intestine
29	chr6:167009200-167013200	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:167009400-167011600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:167009400-167011600	Enhancers	Osteobl	bone
32	chr6:167009400-167011800	Enhancers	Muscle Satellite Cultured Cells	--
33	chr6:167009400-167015800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:167009600-167010800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:167009600-167011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:167009600-167011200	Weak transcription	Fetal Heart	heart
37	chr6:167009600-167011600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:167009600-167011600	Weak transcription	Colon Smooth Muscle	Colon
39	chr6:167009600-167014200	Weak transcription	HMEC	breast
40	chr6:167009600-167014800	Enhancers	NH-A	brain
41	chr6:167009800-167010800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:167009800-167011400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:167009800-167011800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:167009800-167012200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:167009800-167012200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:167010000-167011400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:167010200-167010600	Enhancers	Brain Angular Gyrus	brain
48	chr6:167010200-167010800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr6:167010200-167014000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:167010200-167014000	Enhancers	Lung	lung

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