Variant report

Variant	rs11884249
Chromosome Location	chr2:180362645-180362646
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11885574	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11901927	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12471789	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12620539	0.91[CHB][hapmap]
rs13003114	0.94[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap]
rs13006274	0.87[CEU][hapmap];0.91[CHB][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13016735	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1400819	0.90[CHB][hapmap];0.83[CHD][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs1400822	0.83[CEU][hapmap];0.95[CHB][hapmap]
rs16866761	0.90[CHB][hapmap];0.83[YRI][hapmap]
rs17285077	0.90[CHB][hapmap]
rs17747516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17747613	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2138877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271759	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4893875	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4894100	0.81[ASW][hapmap];0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.84[LWK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6433794	0.83[CHB][hapmap]
rs6708300	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6715181	0.91[CHB][hapmap]
rs6715297	0.87[CEU][hapmap];0.95[CHB][hapmap]
rs6718486	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7563400	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7563476	0.91[CHB][hapmap]
rs9288034	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[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	nsv875468	chr2:180352334-180396869	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv875469	chr2:180354642-180396869	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11884249	PRKRA	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180350600-180367200	Weak transcription	Liver	Liver
2	chr2:180352800-180378400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:180358400-180367800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links