Variant report

Variant	rs9301945
Chromosome Location	chr13:94875308-94875309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1412934	0.80[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap]
rs1886930	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4773782	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9516373	0.81[EUR][1000 genomes]
rs9524380	0.96[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs9524382	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9561517	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948455	chr13:94451368-94988900	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916640	chr13:94521959-95101443	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv533063	chr13:94560362-95101443	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv430599	chr13:94699399-94934930	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv933263	chr13:94711183-94897124	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv526048	chr13:94767311-94880219	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv562754	chr13:94770794-94895346	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	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
rs9301945	GPC6	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94864000-94879800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:94867800-94888000	Weak transcription	Fetal Intestine Small	intestine
3	chr13:94869200-94883400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:94872200-94884000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:94874400-94875800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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Input of quick search could be:

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

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