Variant report

Variant	rs1548653
Chromosome Location	chr12:68360943-68360944
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10735943	1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap]
rs10748092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784660	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10784661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784664	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10878708	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878709	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878710	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878711	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10878717	0.94[ASN][1000 genomes]
rs10878720	0.88[CEU][hapmap]
rs10878721	0.88[CEU][hapmap]
rs10878722	0.89[ASN][1000 genomes]
rs11176957	0.83[AFR][1000 genomes]
rs11176958	0.83[AFR][1000 genomes]
rs11176970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11176976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176977	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176992	0.88[CEU][hapmap]
rs11176995	0.88[CEU][hapmap]
rs1548650	1.00[ASN][1000 genomes]
rs1548651	1.00[ASN][1000 genomes]
rs1548652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1905452	1.00[ASN][1000 genomes]
rs2097999	0.91[ASN][1000 genomes]
rs2190735	0.89[ASN][1000 genomes]
rs2839995	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870964	0.94[ASN][1000 genomes]
rs4141136	0.92[ASN][1000 genomes]
rs4913386	0.95[ASN][1000 genomes]
rs6581784	1.00[ASN][1000 genomes]
rs7310108	0.95[ASN][1000 genomes]
rs7954182	0.91[ASN][1000 genomes]
rs7959275	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7962230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965959	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7979547	0.98[ASN][1000 genomes]
rs7980416	0.82[TSI][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	esv3411149	chr12:68066948-68435533	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1039638	chr12:68293351-68399871	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1548653	NDUFA13	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:68356200-68363200	Weak transcription	Psoas Muscle	Psoas
2	chr12:68356200-68370600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:68359200-68363000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:68359200-68363200	Weak transcription	HSMM	muscle
5	chr12:68359600-68362000	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:68360000-68361000	Enhancers	Colon Smooth Muscle	Colon
7	chr12:68360000-68361200	Enhancers	GM12878-XiMat	blood
8	chr12:68360200-68361200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:68360400-68361000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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