Variant report

Variant	rs199696
Chromosome Location	chr1:77505413-77505414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11162254	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11162255	0.90[ASN][1000 genomes]
rs11162262	0.85[CHD][hapmap];0.88[ASN][1000 genomes]
rs11162265	0.83[ASN][1000 genomes]
rs11162266	0.86[ASN][1000 genomes]
rs12023405	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12084236	0.90[CHB][hapmap];0.90[ASN][1000 genomes]
rs12132230	0.88[ASN][1000 genomes]
rs12731718	0.90[ASN][1000 genomes]
rs175317	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs187956	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs199662	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199663	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199665	0.98[ASN][1000 genomes]
rs199666	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199668	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs199669	0.96[ASN][1000 genomes]
rs199672	0.83[AMR][1000 genomes]
rs199673	0.80[AMR][1000 genomes]
rs199692	0.94[AFR][1000 genomes]
rs199699	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199702	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199704	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs199707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs199709	0.99[ASN][1000 genomes]
rs199716	0.99[ASN][1000 genomes]
rs199717	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs199718	0.99[ASN][1000 genomes]
rs199719	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs199720	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199721	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199722	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199723	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs199724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2003706	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2281305	0.90[CHB][hapmap];0.92[CHD][hapmap];0.90[ASN][1000 genomes]
rs34036815	0.90[ASN][1000 genomes]
rs35224101	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003826	chr1:76965331-77656929	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv535006	chr1:76965331-77656929	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv830292	chr1:77425571-77584307	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77497000-77516800	Weak transcription	Fetal Stomach	stomach
2	chr1:77503400-77505600	Enhancers	Brain Germinal Matrix	brain
3	chr1:77503400-77506400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:77503400-77506600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:77503600-77506400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:77503600-77506800	Enhancers	HMEC	breast
7	chr1:77503800-77505800	Enhancers	Muscle Satellite Cultured Cells	--
8	chr1:77503800-77506200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:77503800-77506200	Enhancers	Rectal Smooth Muscle	rectum
10	chr1:77503800-77512200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:77504000-77506000	Enhancers	Osteobl	bone
12	chr1:77504200-77506000	Enhancers	Colon Smooth Muscle	Colon
13	chr1:77504200-77506200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:77504400-77505800	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr1:77504600-77506000	Enhancers	Stomach Smooth Muscle	stomach
16	chr1:77504600-77506400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:77505000-77506000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:77505000-77506000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:77505000-77506200	Enhancers	HSMMtube	muscle
20	chr1:77505000-77506400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:77505000-77506800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
22	chr1:77505200-77505800	Enhancers	NHEK	skin
23	chr1:77505200-77506200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:77505200-77506200	Enhancers	NH-A	brain
25	chr1:77505200-77506200	Enhancers	NHDF-Ad	bronchial
26	chr1:77505400-77505600	Enhancers	A549	lung
27	chr1:77505400-77505800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:77505400-77506000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:77505400-77506200	Enhancers	HSMM	muscle

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