Variant report

Variant	rs11126552
Chromosome Location	chr2:76916042-76916043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11126553	0.80[ASN][1000 genomes]
rs11126555	0.89[ASN][1000 genomes]
rs11676499	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11680608	0.82[ASN][1000 genomes]
rs11682344	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11687558	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11694778	0.90[ASN][1000 genomes]
rs12467521	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12467593	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12467647	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12467930	0.81[ASN][1000 genomes]
rs12469595	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12471861	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12475638	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13006918	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1519998	0.88[ASN][1000 genomes]
rs17013027	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17013038	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17404655	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17404752	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1879215	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1879216	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1879217	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1879218	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1915043	0.90[ASN][1000 genomes]
rs2037352	0.88[ASN][1000 genomes]
rs34139423	0.88[ASN][1000 genomes]
rs34767571	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35226579	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35383621	0.81[ASN][1000 genomes]
rs35849358	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57829576	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62170373	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62170374	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6716356	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6744896	0.83[ASN][1000 genomes]
rs6745127	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv582235	chr2:76881210-76997763	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv1006275	chr2:76885103-76929056	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1002822	chr2:76885103-76940701	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1010119	chr2:76904730-76949552	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1003119	chr2:76914457-76949552	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	n/a	n/a	inside rSNPs	diseases
6	nsv1003325	chr2:76914457-76957491	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
7	nsv582236	chr2:76914970-76929044	Weak transcription Enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11126552	HTRA2	cis	cerebellum	SCAN
rs11126552	RETSAT	trans	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:76906000-76926600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:76914200-76918200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:76916000-76927800	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links