Variant report

Variant	rs540505
Chromosome Location	chr11:56865255-56865256
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2853083	0.83[MEX][hapmap]
rs493461	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525315	0.89[EUR][1000 genomes]
rs527174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537726	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563813	0.89[EUR][1000 genomes]
rs565066	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs572029	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs637536	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs646724	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs655949	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs668370	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832162	chr11:56716658-56901528	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
2	nsv915640	chr11:56814841-57139786	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv482317	chr11:56857026-57028631	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs540505	OR5M10	cis	parietal	SCAN
rs540505	MS4A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56862000-56865400	Weak transcription	Fetal Heart	heart
2	chr11:56864600-56866600	Enhancers	Ovary	ovary
3	chr11:56864800-56866200	Enhancers	Fetal Lung	lung
4	chr11:56864800-56866400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr11:56864800-56866400	Enhancers	Fetal Stomach	stomach

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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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