Variant report

Variant	rs647809
Chromosome Location	chr1:78661471-78661472
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1407747	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1407748	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1625234	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1770307	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4258184	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4285658	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4650607	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs488469	0.86[AFR][1000 genomes]
rs501774	0.82[AFR][1000 genomes]
rs513977	0.86[AFR][1000 genomes]
rs577978	0.82[AFR][1000 genomes]
rs582795	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs591343	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs597063	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs597272	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs610508	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs618063	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs618581	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs633664	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs634741	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs644332	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs648315	0.84[AMR][1000 genomes]
rs658212	0.83[AFR][1000 genomes]
rs659902	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6665090	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs675799	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs677875	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs680971	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs683097	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs684996	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9425188	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1000388	chr1:78638946-78665285	Enhancers Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
5	nsv546600	chr1:78649862-78666990	Active TSS Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs647809	NEXN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78656600-78668800	Weak transcription	Liver	Liver
2	chr1:78657600-78667200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr1:78657600-78669600	Weak transcription	Pancreas	Pancrea
4	chr1:78659400-78668000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:78661000-78661800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:78661400-78661600	Enhancers	Small Intestine	intestine
7	chr1:78661400-78661800	Enhancers	NHDF-Ad	bronchial

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