Variant report

Variant	rs2712789
Chromosome Location	chr11:74814902-74814903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74812003..74816154-chr11:74816263..74818470,5	K562	blood:
2	chr11:74723507..74725888-chr11:74813976..74816359,2	K562	blood:
3	chr11:74813734..74816663-chr11:74951389..74954189,2	K562	blood:
4	chr11:74805066..74808860-chr11:74814569..74816963,4	K562	blood:
5	chr11:74809645..74812912-chr11:74813164..74816030,5	K562	blood:
6	chr11:74790767..74792368-chr11:74814886..74816678,2	K562	blood:
7	chr11:74658596..74660669-chr11:74813822..74816180,2	K562	blood:

Variant related genes	Relation type
ENSG00000255136	Chromatin interaction
ENSG00000166435	Chromatin interaction
ENSG00000118363	Chromatin interaction
ENSG00000213333	Chromatin interaction
ENSG00000261594	Chromatin interaction
ENSG00000137491	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10899068	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11236316	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236317	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236322	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236323	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236325	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11236359	0.85[CEU][hapmap]
rs1893839	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2187435	0.90[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs2712781	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2712787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2712790	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2712792	0.82[ASN][1000 genomes]
rs2712796	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2712805	0.90[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2712807	0.81[ASN][1000 genomes]
rs2712819	0.85[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap]
rs2851064	0.90[CEU][hapmap];0.80[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs2851074	0.84[CEU][hapmap]
rs2851085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2851094	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851096	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2851102	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2851108	0.89[ASN][1000 genomes]
rs3017932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3018832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34806493	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4146884	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4456280	0.80[CHB][hapmap]
rs7112183	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7122948	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753171	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7933093	0.82[AFR][1000 genomes]
rs949072	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634028	0.84[EUR][1000 genomes];0.94[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2712789	XRRA1	cis	lymphoblastoid	seeQTL
rs2712789	UCP2	cis	parietal	SCAN
rs2712789	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs2712789	PHOX2A	cis	parietal	SCAN
rs2712789	P2RY2	cis	parietal	SCAN
rs2712789	XRRA1	cis	multi-tissue	Pritchard
rs2712789	XRRA1	cis	cerebellum	SCAN
rs2712789	XRRA1	cis	parietal	SCAN
rs2712789	INPPL1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74811600-74818200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr11:74811800-74816600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr11:74811800-74816600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:74812000-74816400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr11:74812400-74816200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:74814200-74815200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr11:74814200-74815200	Enhancers	NHDF-Ad	bronchial
8	chr11:74814400-74815000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr11:74814400-74815000	Enhancers	GM12878-XiMat	blood
10	chr11:74814400-74815000	Enhancers	HSMM	muscle
11	chr11:74814400-74815200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr11:74814400-74815200	Flanking Active TSS	K562	blood
13	chr11:74814400-74815200	Enhancers	NH-A	brain
14	chr11:74814400-74815200	Enhancers	NHLF	lung
15	chr11:74814400-74815200	Enhancers	Osteobl	bone
16	chr11:74814600-74815000	Enhancers	HUVEC	blood vessel
17	chr11:74814800-74815000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr11:74814800-74815200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr11:74814800-74815200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:74814800-74815200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:74814800-74815200	Flanking Active TSS	A549	lung
22	chr11:74814800-74815200	Enhancers	HMEC	breast
23	chr11:74814800-74818200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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