Variant report

Variant	rs2249090
Chromosome Location	chr15:56558014-56558015
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56535639..56539237-chr15:56554453..56558702,5	K562	blood:

Variant related genes	Relation type
ENSG00000151575	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11630363	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap]
rs11855094	0.87[CHB][hapmap]
rs12900678	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs12905782	0.84[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs12905899	0.92[CEU][hapmap]
rs12911094	0.85[CEU][hapmap]
rs12911427	0.91[CEU][hapmap]
rs1372753	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs1402177	0.84[AMR][1000 genomes]
rs1477590	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs1549452	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs16976890	0.87[CHB][hapmap]
rs17819438	0.92[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2119937	0.84[CEU][hapmap]
rs2303441	0.92[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs2460650	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2465973	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2554287	0.87[CHB][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap]
rs2682012	0.84[ASN][1000 genomes]
rs2682019	0.84[AMR][1000 genomes]
rs2682049	0.81[AMR][1000 genomes]
rs2682051	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2682053	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2682054	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs2682059	0.92[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2713924	0.92[CEU][hapmap]
rs2713931	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2713933	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2713936	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2713941	0.92[CEU][hapmap]
rs2718921	0.87[CHB][hapmap]
rs2718934	0.92[CEU][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2718941	0.92[CEU][hapmap]
rs2725854	0.88[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2725856	1.00[YRI][hapmap]
rs2947020	0.81[ASN][1000 genomes]
rs2947021	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3784552	0.88[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap]
rs3817406	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs4310791	0.92[CEU][hapmap];0.91[MEX][hapmap]
rs4310792	0.96[CEU][hapmap]
rs4774232	0.92[CEU][hapmap]
rs6493856	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap]
rs6493858	0.88[CEU][hapmap];0.87[CHB][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.95[TSI][hapmap]
rs7170307	0.92[ASW][hapmap];0.81[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap]
rs7181235	0.87[CHB][hapmap]
rs7496025	0.92[CEU][hapmap]
rs795791	0.82[CHB][hapmap]
rs795800	0.87[CHB][hapmap]
rs8024031	0.85[CEU][hapmap]
rs9672886	0.88[CEU][hapmap]

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	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2249090	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs2249090	FLJ12994	cis	multi-tissue	Pritchard

Chromatin state (count:0 , 50 per page) page:

No data

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links