Variant report

Variant	rs6049888
Chromosome Location	chr20:24685589-24685590
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11087477	0.80[ASN][1000 genomes]
rs11698370	0.81[ASN][1000 genomes]
rs11698382	0.80[ASN][1000 genomes]
rs11699163	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11699367	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11699717	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11699876	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12625030	0.95[CEU][hapmap]
rs13043903	0.80[ASN][1000 genomes]
rs34084123	0.84[ASN][1000 genomes]
rs34489305	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35449981	0.80[ASN][1000 genomes]
rs4140548	0.95[CEU][hapmap]
rs57130956	0.80[ASN][1000 genomes]
rs57927783	0.83[ASN][1000 genomes]
rs59210731	0.80[ASN][1000 genomes]
rs6036878	0.95[CEU][hapmap]
rs6049859	0.94[CEU][hapmap]
rs6049860	0.95[CEU][hapmap]
rs6049868	0.95[CEU][hapmap]
rs6049869	0.95[CEU][hapmap]
rs6049871	0.95[CEU][hapmap]
rs6049872	0.84[CEU][hapmap]
rs6049874	0.95[CEU][hapmap]
rs729540	0.95[CEU][hapmap]
rs735186	0.95[CEU][hapmap]
rs742807	0.95[CEU][hapmap]
rs880502	0.95[CEU][hapmap]
rs926708	0.80[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	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv523138	chr20:24683554-24686375	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6049888	TMEM90B	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24675800-24689200	Weak transcription	Right Atrium	heart
2	chr20:24685000-24685800	Enhancers	Thymus	Thymus
3	chr20:24685400-24685800	Enhancers	Fetal Thymus	thymus

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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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