Variant report

Variant	rs9823822
Chromosome Location	chr3:159074327-159074328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1122205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11921343	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1349165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs1349166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap]
rs1449018	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap]
rs1449019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs1449025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1530726	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1823311	0.93[CEU][hapmap]
rs1868415	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1968645	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2365820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2365821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35886259	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4440163	0.86[CEU][hapmap]
rs6441253	0.81[CEU][hapmap]
rs6441254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6771767	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6777541	0.93[CEU][hapmap]
rs6780514	0.86[ASW][hapmap];0.93[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap]
rs6781221	0.81[CEU][hapmap]
rs6807305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6810169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7611870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7629577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7629583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630467	0.91[CEU][hapmap]
rs7651493	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9283610	0.81[CEU][hapmap]
rs9283611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9290036	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9290041	0.80[EUR][1000 genomes]
rs9290042	0.86[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs9681445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9809459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9821641	0.83[CHB][hapmap]
rs9825664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9831067	0.81[CEU][hapmap]
rs9832614	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9834337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9838646	0.81[CEU][hapmap]
rs9855118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9865361	0.93[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap]
rs9867432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9871574	0.93[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9873091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874504	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9874862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159073400-159074400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:159073800-159076400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr3:159074000-159075400	Enhancers	Brain Angular Gyrus	brain
4	chr3:159074000-159075400	Enhancers	Brain Hippocampus Middle	brain
5	chr3:159074000-159075400	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr3:159074000-159075800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:159074000-159076400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:159074200-159074600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:159074200-159074600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:159074200-159075800	Enhancers	Brain Anterior Caudate	brain
11	chr3:159074200-159075800	Enhancers	Brain Cingulate Gyrus	brain

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