Variant report

Variant	rs6760462
Chromosome Location	chr2:114057872-114057873
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10201645	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10209795	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11123174	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11123175	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11679928	0.85[AMR][1000 genomes]
rs11683025	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11687706	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11688620	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11889663	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12467534	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12989922	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13002606	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13022812	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13385108	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13388160	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17626470	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34657362	0.93[ASN][1000 genomes]
rs4091938	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848324	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4848325	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4848326	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4848327	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4848328	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4848329	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4848330	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4849191	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4849192	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4849194	0.80[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6753679	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6760648	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7587376	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

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	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv961872	chr2:114041837-114061641	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2762785	chr2:114044712-114081784	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6760462	PAX8	cis	Esophagus Muscularis	GTEx
rs6760462	LOC654433	cis	cerebellum	SCAN
rs6760462	PAX8	cis	multi-tissue	Pritchard
rs6760462	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs6760462	AC016683.6	cis	Muscle Skeletal	GTEx
rs6760462	AC016683.6	cis	Whole Blood	GTEx
rs6760462	PAX8	cis	lymphoblastoid	seeQTL
rs6760462	LOC654433	cis	parietal	SCAN
rs6760462	AC016683.6	cis	Esophagus Mucosa	GTEx
rs6760462	AC016683.6	cis	Nerve Tibial	GTEx
rs6760462	AC016683.6	cis	lung	GTEx
rs6760462	PAX8	cis	lung	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114055000-114062400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:114057600-114058000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:114057800-114058400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links