Variant report

Variant	rs2462906
Chromosome Location	chr7:27120109-27120110
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10238645	0.81[EUR][1000 genomes]
rs10242754	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11563327	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs17471088	0.85[EUR][1000 genomes]
rs17471457	0.86[CHB][hapmap]
rs2079138	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2248744	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2253415	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2254463	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2264802	0.81[EUR][1000 genomes]
rs2428416	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2428417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2428418	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2428421	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2428425	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2428431	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2462902	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2462908	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2465264	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2465266	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2465270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2465274	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2522824	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2522825	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2522826	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2693659	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2693665	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2693668	0.81[EUR][1000 genomes]
rs2712234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2712238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2712242	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2712246	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2712248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34725546	0.81[ASN][1000 genomes]
rs55889667	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv824038	chr7:27119294-27284522	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription 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	183 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2462906	HOTAIRM1	cis	Whole Blood	GTEx
rs2462906	HOXA2	cis	Whole Blood	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27118400-27120400	Enhancers	NHEK	skin
2	chr7:27118400-27122600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr7:27118800-27121400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:27118800-27122600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:27118800-27122800	Enhancers	HMEC	breast
6	chr7:27119000-27120400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr7:27119000-27122600	Enhancers	Hela-S3	cervix
8	chr7:27119200-27120400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:27119200-27121000	Enhancers	HepG2	liver
10	chr7:27119200-27121800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:27119200-27127600	Weak transcription	Osteobl	bone
12	chr7:27119400-27120600	Weak transcription	Fetal Intestine Small	intestine
13	chr7:27119400-27121000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:27119600-27125000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:27119800-27120200	Weak transcription	Fetal Intestine Large	intestine
16	chr7:27119800-27120200	Weak transcription	A549	lung
17	chr7:27120000-27120400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:27120000-27121000	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links