Variant report

Variant	rs10276952
Chromosome Location	chr7:27105629-27105630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10257437	0.82[CEU][hapmap]
rs10257464	0.87[CEU][hapmap]
rs11977871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12673984	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12674308	0.96[ASN][1000 genomes]
rs12700771	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12700785	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13221446	0.92[AFR][1000 genomes]
rs13230726	0.96[EUR][1000 genomes]
rs17427218	0.95[ASN][1000 genomes]
rs17436757	0.80[ASN][1000 genomes]
rs17436827	0.83[ASN][1000 genomes]
rs17437154	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs17448911	1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs17500459	0.89[AFR][1000 genomes]
rs213515	0.84[YRI][hapmap]
rs213516	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes]
rs2140998	0.85[YRI][hapmap]
rs2259141	1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2301719	0.94[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2648079	0.84[EUR][1000 genomes]
rs2693660	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2693661	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2693669	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2712235	0.82[YRI][hapmap]
rs2712243	0.82[AFR][1000 genomes]
rs28357116	0.92[ASN][1000 genomes]
rs2936424	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2936425	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62454362	0.92[ASN][1000 genomes]
rs62454371	0.95[ASN][1000 genomes]
rs62454372	0.90[ASN][1000 genomes]
rs62454374	0.90[ASN][1000 genomes]
rs62454375	0.90[ASN][1000 genomes]
rs62457403	0.80[ASN][1000 genomes]
rs62457404	0.91[ASN][1000 genomes]
rs6461982	0.85[YRI][hapmap]
rs6948446	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6953314	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs706015	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs706019	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs774244	0.85[EUR][1000 genomes]
rs774245	0.85[EUR][1000 genomes]
rs774249	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs774250	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs774251	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs774252	0.82[CEU][hapmap];0.84[YRI][hapmap]
rs774253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs774256	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs774263	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs774265	0.81[CEU][hapmap];0.83[YRI][hapmap]
rs774266	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7791056	0.82[CEU][hapmap];0.84[YRI][hapmap]
rs7797624	0.89[AFR][1000 genomes]
rs954051	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
3	nsv1018709	chr7:26990384-27216552	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
4	nsv538806	chr7:26990384-27216552	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	nsv887856	chr7:27073731-27297791	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	183 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10276952	HOXA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27103600-27106000	Enhancers	NHDF-Ad	bronchial
2	chr7:27103800-27106000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr7:27103800-27106800	Enhancers	Osteobl	bone
4	chr7:27104000-27106400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr7:27104200-27106800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:27104400-27105800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:27105000-27106600	Enhancers	NHEK	skin
8	chr7:27105200-27105800	Enhancers	HSMM	muscle
9	chr7:27105200-27106400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr7:27105400-27105800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:27105400-27106000	Flanking Active TSS	Hela-S3	cervix
12	chr7:27105400-27106000	Enhancers	HMEC	breast
13	chr7:27105400-27106000	Enhancers	HUVEC	blood vessel

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