Variant report

Variant	rs7966543
Chromosome Location	chr12:66484329-66484330
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10878373	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11176028	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11176057	1.00[ASW][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs1168745	0.95[CEU][hapmap];1.00[GIH][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap]
rs1168754	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1168769	0.82[EUR][1000 genomes]
rs1732886	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs1732887	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs1732888	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs1921079	0.82[EUR][1000 genomes]
rs2701652	0.86[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs2870784	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73123417	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7952988	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953500	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966800	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974467	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8793	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899213	chr12:66389968-66500036	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv832446	chr12:66393863-66501484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1049537	chr12:66403269-66606174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7966543	RP11-745O10.2	cis	Thyroid	GTEx
rs7966543	RP11-745O10.2	cis	Heart Left Ventricle	GTEx
rs7966543	RP11-745O10.2	cis	lung	GTEx
rs7966543	RP11-745O10.2	cis	Muscle Skeletal	GTEx
rs7966543	IRAK3	cis	lymphoblastoid	seeQTL
rs7966543	RP11-745O10.2	cis	Whole Blood	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66468800-66486000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:66481200-66486000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:66481200-66486400	Weak transcription	NH-A	brain
4	chr12:66481200-66486400	Weak transcription	NHDF-Ad	bronchial
5	chr12:66481400-66486000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:66481400-66486000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:66481400-66486000	Weak transcription	Osteobl	bone
8	chr12:66481400-66486400	Weak transcription	HSMM	muscle
9	chr12:66481600-66486000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:66481600-66486000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:66484000-66484600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:66484200-66486400	Weak transcription	HUVEC	blood vessel

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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