Variant report

Variant	rs1893839
Chromosome Location	chr11:74812021-74812022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74812003..74816154-chr11:74816263..74818470,5	K562	blood:
2	chr11:74740096..74742646-chr11:74811856..74813625,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10899068	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11236316	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236317	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236322	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11236323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236325	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236359	0.85[CEU][hapmap]
rs2187435	0.90[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2712781	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2712787	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2712789	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2712790	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2712792	0.80[ASN][1000 genomes]
rs2712796	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2712805	0.90[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2712807	0.82[ASN][1000 genomes]
rs2712819	0.85[CEU][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs2851064	0.90[CEU][hapmap];0.85[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs2851074	0.84[CEU][hapmap]
rs2851085	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851094	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2851096	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2851102	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2851108	0.86[ASN][1000 genomes]
rs3017932	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3018832	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34806493	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4146884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4456280	0.85[CHB][hapmap]
rs7112183	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7122948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753171	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs949072	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9634028	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[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	esv3478707	chr11:74782633-74842791	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
2	esv3478718	chr11:74782633-74842791	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1893839	PHOX2A	cis	parietal	SCAN
rs1893839	INPPL1	cis	parietal	SCAN
rs1893839	UCP2	cis	parietal	SCAN
rs1893839	XRRA1	cis	parietal	SCAN
rs1893839	XRRA1	cis	multi-tissue	Pritchard
rs1893839	XRRA1	cis	lymphoblastoid	seeQTL
rs1893839	P2RY2	cis	parietal	SCAN
rs1893839	XRRA1	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74808000-74814800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:74811000-74812200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:74811200-74812200	Flanking Active TSS	K562	blood
4	chr11:74811400-74812200	Flanking Active TSS	A549	lung
5	chr11:74811600-74812200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr11:74811600-74812400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr11:74811600-74818200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:74811800-74814400	Weak transcription	HSMM	muscle
9	chr11:74811800-74816600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:74811800-74816600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:74812000-74813200	Active TSS	GM12878-XiMat	blood
12	chr11:74812000-74814200	Weak transcription	NHDF-Ad	bronchial
13	chr11:74812000-74814400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr11:74812000-74814400	Weak transcription	Osteobl	bone
15	chr11:74812000-74814800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:74812000-74816400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links