Variant report

Variant	rs2960784
Chromosome Location	chr7:26950905-26950906
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1005977	0.81[EUR][1000 genomes]
rs10231265	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10267442	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1082313	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11975480	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13311400	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2015424	0.85[EUR][1000 genomes]
rs2030137	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213514	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs213520	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs213527	0.82[LWK][hapmap]
rs213532	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2252947	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2264680	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2428420	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2428424	0.83[EUR][1000 genomes]
rs2428426	0.81[EUR][1000 genomes]
rs2428428	0.81[EUR][1000 genomes]
rs2428430	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2462901	0.92[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2462903	0.84[EUR][1000 genomes]
rs2462905	0.80[EUR][1000 genomes]
rs2462907	0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap]
rs2465263	0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.91[YRI][hapmap]
rs2465265	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs2465267	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2522822	0.92[CEU][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2522823	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2522829	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2693658	0.85[EUR][1000 genomes]
rs2693666	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2712231	0.88[CEU][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2712232	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2712235	0.92[CEU][hapmap]
rs2712240	0.82[EUR][1000 genomes]
rs2712241	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2712243	0.84[EUR][1000 genomes]
rs2936426	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960785	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2960786	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3807592	0.82[CHB][hapmap]
rs71521786	0.87[ASN][1000 genomes]
rs774245	0.86[AFR][1000 genomes]
rs774248	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs774254	0.92[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs774255	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs774264	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774267	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs774269	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs799237	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2960784	HOTAIRM1	cis	Whole Blood	GTEx
rs2960784	HOXA-AS2	cis	Whole Blood	GTEx
rs2960784	HOXA2	cis	Whole Blood	GTEx
rs2960784	SKAP2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26949600-26951200	Weak transcription	Primary B cells from cord blood	blood
2	chr7:26950000-26952400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr7:26950400-26951000	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr7:26950400-26951600	Weak transcription	HepG2	liver
5	chr7:26950400-26951800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:26950400-26952200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr7:26950400-26956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:26950400-26957400	Weak transcription	NHEK	skin
9	chr7:26950400-26957600	Weak transcription	HMEC	breast
10	chr7:26950600-26951600	Weak transcription	Hela-S3	cervix
11	chr7:26950600-26958000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr7:26950600-26958400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:26950800-26951600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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