Variant report

Variant	rs6542260
Chromosome Location	chr2:116163121-116163122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1037205	0.80[ASN][1000 genomes]
rs11123307	0.80[ASN][1000 genomes]
rs11674650	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11675299	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11675990	0.86[ASN][1000 genomes]
rs11680996	0.86[ASN][1000 genomes]
rs11683441	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12476869	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12614808	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12711825	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13010997	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13016837	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13021167	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1517369	0.90[ASN][1000 genomes]
rs1517370	0.88[ASN][1000 genomes]
rs1517372	0.93[ASN][1000 genomes]
rs1521076	0.93[ASN][1000 genomes]
rs1521079	0.90[ASN][1000 genomes]
rs1589084	0.86[ASN][1000 genomes]
rs1589085	0.86[ASN][1000 genomes]
rs1589086	0.86[ASN][1000 genomes]
rs1626545	0.90[ASN][1000 genomes]
rs1711995	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1712012	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1717037	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1717038	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1717045	0.90[ASN][1000 genomes]
rs1717047	0.86[ASN][1000 genomes]
rs1717055	0.86[ASN][1000 genomes]
rs1829229	0.86[ASN][1000 genomes]
rs2030440	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2030441	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2138776	0.84[ASN][1000 genomes]
rs2677290	0.93[ASN][1000 genomes]
rs2683794	0.88[ASN][1000 genomes]
rs34790955	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34825131	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35275337	0.84[ASN][1000 genomes]
rs56280083	0.84[ASN][1000 genomes]
rs60118669	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs62164391	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62166081	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs708647	0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs708649	0.90[ASN][1000 genomes]
rs843381	0.90[ASN][1000 genomes]
rs843388	0.90[ASN][1000 genomes]
rs843391	0.88[ASN][1000 genomes]
rs843395	0.86[ASN][1000 genomes]
rs843398	0.91[ASN][1000 genomes]
rs843399	0.88[ASN][1000 genomes]
rs843405	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs843408	0.82[ASN][1000 genomes]
rs843412	0.88[ASN][1000 genomes]
rs952747	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874918	chr2:116098665-116183946	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	n/a	n/a	inside rSNPs	diseases
2	nsv874919	chr2:116130709-116219686	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:116155600-116170200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:116160200-116163400	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:116160200-116164600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr2:116161400-116164600	Weak transcription	Fetal Intestine Small	intestine
5	chr2:116162800-116163200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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