Variant report

Variant	rs2762107
Chromosome Location	chr13:94052346-94052347
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11617476	1.00[JPT][hapmap]
rs1323975	1.00[JPT][hapmap]
rs1323985	1.00[JPT][hapmap]
rs1323988	1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[YRI][hapmap]
rs1373835	1.00[JPT][hapmap]
rs1408209	1.00[JPT][hapmap]
rs1408218	1.00[ASN][1000 genomes]
rs1408219	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1924385	0.89[ASN][1000 genomes]
rs2762095	1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2762096	1.00[ASN][1000 genomes]
rs2762097	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs2762099	1.00[ASN][1000 genomes]
rs2762100	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2762106	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2762109	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2762110	1.00[JPT][hapmap]
rs2762111	1.00[JPT][hapmap]
rs2762114	1.00[JPT][hapmap]
rs2762116	1.00[JPT][hapmap]
rs2762117	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2813608	1.00[JPT][hapmap]
rs2813609	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[ASN][1000 genomes]
rs2813610	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs2813615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4142601	1.00[JPT][hapmap]
rs4773740	0.89[ASN][1000 genomes]
rs4773741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs4773742	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7324202	1.00[JPT][hapmap]
rs7982827	1.00[JPT][hapmap]
rs7992679	1.00[JPT][hapmap]
rs8001600	1.00[JPT][hapmap]
rs942350	0.89[ASN][1000 genomes]
rs9524017	1.00[JPT][hapmap]
rs9524021	1.00[JPT][hapmap]
rs9524023	0.89[ASN][1000 genomes]
rs9524025	0.84[ASN][1000 genomes]
rs9524030	0.89[ASN][1000 genomes]
rs9561321	1.00[JPT][hapmap]
rs995811	1.00[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
rs2762107	C9orf80	trans	parietal	SCAN

Chromatin state (count:4 , 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	chr13:94050800-94053000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr13:94051600-94055600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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