Variant report

Variant	rs9548849
Chromosome Location	chr13:40212046-40212047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs4329796	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4346098	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4570710	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs7988187	0.92[EUR][1000 genomes]
rs7989518	0.92[EUR][1000 genomes]
rs9315726	0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9548874	0.87[EUR][1000 genomes]
rs9548882	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9548886	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9548887	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs9548889	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9548890	0.90[EUR][1000 genomes]
rs9548892	0.89[EUR][1000 genomes]
rs9566464	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9566468	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9576878	1.00[CEU][hapmap];0.94[CHB][hapmap]
rs9576879	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9576883	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9576885	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9576886	0.86[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9576888	0.92[EUR][1000 genomes];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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
5	esv3363652	chr13:40199001-40221148	Enhancers ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548849	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs9548849	COG6	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40209200-40212800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:40211600-40212200	Enhancers	K562	blood

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