Variant report

Variant	rs7317246
Chromosome Location	chr13:94050926-94050927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10508000	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10508001	0.90[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10508002	0.90[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10508003	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10508004	0.90[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs10508005	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs10851334	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11070059	0.80[EUR][1000 genomes]
rs11618179	0.84[CHD][hapmap];0.92[JPT][hapmap]
rs11619994	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11838734	0.81[EUR][1000 genomes]
rs11841335	0.81[EUR][1000 genomes]
rs11843793	0.90[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs12583509	0.80[EUR][1000 genomes]
rs12584941	0.83[ASN][1000 genomes]
rs12585159	0.80[EUR][1000 genomes]
rs12854387	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12855239	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12855671	0.81[EUR][1000 genomes]
rs12860734	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12866595	0.81[EUR][1000 genomes]
rs12870555	0.90[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs12873979	0.80[EUR][1000 genomes]
rs12874982	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12875395	0.85[EUR][1000 genomes]
rs12876057	0.81[EUR][1000 genomes]
rs12877660	0.81[EUR][1000 genomes]
rs16948775	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16948800	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16948803	0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs16952683	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17188977	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17188998	0.83[ASN][1000 genomes]
rs17267683	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17267711	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17267738	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17267745	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1886205	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2762088	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2762091	0.84[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2762098	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]
rs2762108	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2762112	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2762115	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2892657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33961779	0.92[JPT][hapmap]
rs34119608	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34136695	0.81[EUR][1000 genomes]
rs35048964	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4378503	0.81[ASN][1000 genomes]
rs4644730	0.82[EUR][1000 genomes]
rs5005454	0.90[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5005455	0.84[ASN][1000 genomes]
rs56228951	0.81[EUR][1000 genomes]
rs61964172	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61964173	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61964175	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61964180	0.84[ASN][1000 genomes]
rs7321999	0.92[JPT][hapmap]
rs7325511	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7325937	0.90[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7329962	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7331613	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7334839	0.90[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs7337911	0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs7338634	0.90[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73552665	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74108531	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7994743	0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7998675	0.90[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7998856	0.90[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs7999019	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7999482	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8000632	0.81[EUR][1000 genomes]
rs8000712	0.90[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs8000987	0.81[EUR][1000 genomes]
rs920954	0.81[EUR][1000 genomes]
rs920955	0.90[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs958053	0.90[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][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	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
rs7317246	GPC6	cis	Thyroid	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94046600-94052400	Weak transcription	Fetal Brain Male	brain
2	chr13:94047800-94057200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:94049600-94051400	Enhancers	Osteobl	bone
4	chr13:94050000-94051000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr13:94050200-94051000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr13:94050200-94051000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr13:94050200-94051000	Enhancers	Fetal Heart	heart
8	chr13:94050200-94051800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:94050600-94051400	Enhancers	Adipose Nuclei	Adipose
10	chr13:94050600-94051600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr13:94050600-94052000	Enhancers	A549	lung
12	chr13:94050800-94051600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr13:94050800-94053000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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