Variant report

Variant	rs6492664
Chromosome Location	chr13:94148882-94148883
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11620291	0.94[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12871207	0.87[ASN][1000 genomes]
rs12876880	1.00[JPT][hapmap]
rs1445270	0.81[ASW][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap]
rs17189012	1.00[CHB][hapmap]
rs17267801	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs4400922	0.85[YRI][hapmap]
rs72640578	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72640597	0.83[EUR][1000 genomes]
rs8000028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561374	0.94[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
6	nsv562749	chr13:94083352-94263206	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv900920	chr13:94088707-94151937	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv1842896	chr13:94095160-94153194	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv948714	chr13:94100104-94699435	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv900921	chr13:94105666-94157481	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv900922	chr13:94105666-94281492	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6492664	GPR180	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:94148400-94149000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr13:94148400-94149000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr13:94148600-94149000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr13:94148600-94149400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
5	chr13:94148600-94149400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:94148600-94150000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:94148800-94149000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr13:94148800-94149000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr13:94148800-94149400	Enhancers	Fetal Intestine Large	intestine
10	chr13:94148800-94149400	Enhancers	Fetal Intestine Small	intestine
11	chr13:94148800-94149600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr13:94148800-94149600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:94148800-94149600	Enhancers	HUES64 Cell Line	embryonic stem cell

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

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