Variant report

Variant	rs12671522
Chromosome Location	chr7:28020731-28020732
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10951189	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12537454	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537684	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12671110	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35846584	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38502	0.83[ASN][1000 genomes]
rs38504	0.91[CHB][hapmap];0.87[CHD][hapmap]
rs38507	0.81[ASN][1000 genomes]
rs38513	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs38514	0.82[JPT][hapmap]
rs38517	0.83[CHD][hapmap]
rs4308621	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4357200	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4365989	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4422694	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4492256	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57551874	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59599535	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs66642060	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67479305	0.88[ASN][1000 genomes]
rs6965213	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73089188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73089199	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73301367	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1024819	chr7:27949955-28020969	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12671522	HOXA9	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:28000600-28021600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:28002800-28034600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:28006200-28024800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:28006400-28031800	Weak transcription	NHDF-Ad	bronchial
5	chr7:28009800-28021600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr7:28012400-28022200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:28012400-28028000	Weak transcription	Primary B cells from peripheral blood	blood
8	chr7:28013400-28034200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:28015600-28032400	Weak transcription	Ovary	ovary
10	chr7:28017600-28021800	Weak transcription	Left Ventricle	heart
11	chr7:28017600-28042400	Weak transcription	Aorta	Aorta
12	chr7:28017800-28028000	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:28018000-28026200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:28020000-28032400	Weak transcription	Primary B cells from cord blood	blood

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