Variant report

Variant	rs2762098
Chromosome Location	chr13:94054621-94054622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10508001	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs10508002	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs10508003	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs10508004	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs10508005	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs11618179	0.84[CHD][hapmap];0.92[JPT][hapmap]
rs11619994	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs11843793	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs12855239	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs12870555	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs12875395	0.81[EUR][1000 genomes]
rs16948803	0.81[CHB][hapmap]
rs16952683	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs17267683	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs1886205	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2762088	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2762091	0.84[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2762108	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2762112	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2762115	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2892657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33961779	0.92[JPT][hapmap]
rs5005454	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs7317246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7321999	0.92[JPT][hapmap]
rs7325937	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs7334839	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs7338634	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs7994743	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs7998675	0.90[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap]
rs7998856	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs8000712	0.90[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap]
rs920955	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs958053	0.90[CHB][hapmap];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	nsv869070	chr13:93347616-94286933	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1053035	chr13:93842576-94229732	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541880	chr13:93842576-94229732	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv530636	chr13:93997311-94281707	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv916039	chr13:94035909-94191105	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2762098	GPC6	cis	Thyroid	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94047800-94057200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:94051600-94055600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr13:94053800-94058000	Weak transcription	Fetal Brain Male	brain
4	chr13:94054200-94054800	Enhancers	Fetal Brain Female	brain
5	chr13:94054400-94055000	Enhancers	Aorta	Aorta
6	chr13:94054400-94055000	Enhancers	Fetal Kidney	kidney

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