Variant report

Variant	rs16881901
Chromosome Location	chr5:9062943-9062944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11134348	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739474	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741186	0.90[YRI][hapmap]
rs11742324	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745238	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11954862	0.89[ASN][1000 genomes]
rs12516982	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520615	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521925	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354570	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881875	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881898	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881912	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881913	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881928	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16881943	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902809	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947584	0.89[ASN][1000 genomes]
rs2290735	1.00[CHD][hapmap];0.95[GIH][hapmap]
rs2388001	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388004	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388005	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36195254	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6871654	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6889183	0.89[ASN][1000 genomes]
rs7727526	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS 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	9 gene(s)	inside rSNPs	diseases
8	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9038800-9063600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr5:9040200-9064600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:9040800-9122000	Weak transcription	Colonic Mucosa	Colon
4	chr5:9042200-9066600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:9044800-9065200	Weak transcription	Pancreas	Pancrea
6	chr5:9046600-9065400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:9050000-9065200	Weak transcription	Right Ventricle	heart
8	chr5:9051000-9065200	Weak transcription	Left Ventricle	heart
9	chr5:9051800-9065200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:9053200-9067400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr5:9053800-9077800	Weak transcription	Fetal Heart	heart
12	chr5:9056400-9069000	Weak transcription	Lung	lung
13	chr5:9057200-9069200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr5:9059200-9063000	Weak transcription	Dnd41	blood
15	chr5:9059200-9064000	Weak transcription	Brain Angular Gyrus	brain
16	chr5:9060200-9066600	Strong transcription	Liver	Liver
17	chr5:9060400-9063600	Strong transcription	Fetal Intestine Small	intestine
18	chr5:9060400-9066600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:9060400-9066800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:9060600-9066600	Strong transcription	Fetal Stomach	stomach
21	chr5:9060600-9067600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:9060800-9063600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:9060800-9063600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:9060800-9067000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:9060800-9067000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:9060800-9077000	Weak transcription	Ovary	ovary
27	chr5:9060800-9085600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:9061000-9063600	Weak transcription	NH-A	brain
29	chr5:9061200-9064400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:9061200-9067600	Weak transcription	Osteobl	bone
31	chr5:9061400-9063200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:9061400-9063200	Weak transcription	NHDF-Ad	bronchial
33	chr5:9061400-9065800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:9061400-9066600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr5:9061600-9063600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr5:9061600-9066600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:9061800-9063000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:9061800-9063000	Strong transcription	Brain Hippocampus Middle	brain
39	chr5:9061800-9063600	Strong transcription	Fetal Muscle Leg	muscle
40	chr5:9061800-9067000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:9061800-9067000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr5:9062000-9063400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:9062000-9065200	Weak transcription	Aorta	Aorta
44	chr5:9062000-9070000	Weak transcription	Fetal Lung	lung
45	chr5:9062200-9066000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr5:9062400-9063200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr5:9062400-9063600	Strong transcription	NHLF	lung
48	chr5:9062600-9063000	ZNF genes & repeats	Esophagus	oesophagus
49	chr5:9062600-9063200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:9062600-9063800	Strong transcription	Rectal Mucosa Donor 31	rectum

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