Variant report

Variant	rs1876690
Chromosome Location	chr5:57924997-57924998
allele	A/T
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:42)

rs_ID	r²[population]
rs10038836	1.00[AFR][1000 genomes]
rs10055378	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10055388	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10055649	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10058168	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10060872	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10066482	1.00[AFR][1000 genomes]
rs10070606	0.87[AFR][1000 genomes]
rs10071864	0.84[EUR][1000 genomes]
rs10077599	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10078211	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10079823	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10471459	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10472068	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10472069	0.83[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10472070	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10514876	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10514877	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11750820	1.00[AFR][1000 genomes]
rs11750857	0.87[AFR][1000 genomes]
rs12152774	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12153291	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13354829	1.00[AFR][1000 genomes]
rs13358097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13436622	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17280328	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17280636	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17282012	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17348080	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2194037	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2279981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35694320	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs5011219	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6877247	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72760270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72760285	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72760294	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs753219	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs753220	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9283719	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9292171	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292173	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1029145	chr5:57905821-58141221	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830311	chr5:57912546-58105636	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57919800-57925000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:57921000-57933000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:57924000-57925400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:57924000-57925400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:57924200-57925400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:57924200-57925400	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr5:57924200-57925600	Enhancers	Adipose Nuclei	Adipose
8	chr5:57924200-57925600	Enhancers	Pancreas	Pancrea
9	chr5:57924200-57926000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr5:57924200-57926000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr5:57924200-57926200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr5:57924200-57927200	Enhancers	Fetal Intestine Large	intestine
13	chr5:57924200-57927200	Enhancers	Fetal Intestine Small	intestine
14	chr5:57924200-57928400	Enhancers	Stomach Mucosa	stomach
15	chr5:57924400-57925600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:57924400-57925600	Enhancers	Gastric	stomach
17	chr5:57924400-57925800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr5:57924400-57925800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:57924400-57925800	Enhancers	Fetal Stomach	stomach
20	chr5:57924400-57926000	Enhancers	Brain Germinal Matrix	brain
21	chr5:57924400-57926000	Enhancers	Fetal Lung	lung
22	chr5:57924400-57926000	Enhancers	Small Intestine	intestine
23	chr5:57924400-57926200	Enhancers	Liver	Liver
24	chr5:57924600-57925200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:57924600-57925400	Weak transcription	Right Atrium	heart
26	chr5:57924600-57925600	Enhancers	Colonic Mucosa	Colon

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