Variant report

Variant	rs1509997
Chromosome Location	chr11:56463059-56463060
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10896502	0.85[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs10896513	0.95[MEX][hapmap]
rs11228656	0.85[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs11228677	0.85[CHB][hapmap];0.80[CHD][hapmap];0.82[JPT][hapmap]
rs11228700	0.83[ASN][1000 genomes]
rs11228715	0.85[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.89[MKK][hapmap]
rs12363217	0.81[ASN][1000 genomes]
rs1397048	1.00[MEX][hapmap]
rs2000932	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs35455046	0.85[ASN][1000 genomes]
rs35640105	0.83[ASN][1000 genomes]
rs3867254	0.82[AMR][1000 genomes]
rs4939077	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs4939082	0.82[ASN][1000 genomes]
rs55848395	0.80[AMR][1000 genomes]
rs949367	0.85[CHB][hapmap];0.82[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	nsv1050024	chr11:55900482-56518943	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
2	nsv497854	chr11:55917298-56537994	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv949349	chr11:56371633-56593610	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1051853	chr11:56393347-56523720	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv975115	chr11:56460276-56468712	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1509997	OR10Q1	cis	cerebellum	SCAN
rs1509997	MS4A3	cis	cerebellum	SCAN
rs1509997	TIMM10	cis	cerebellum	SCAN
rs1509997	OR5B2	cis	parietal	SCAN
rs1509997	OR5AK2	cis	cerebellum	SCAN
rs1509997	SLC43A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56461400-56465400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:56462600-56463400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:56463000-56464000	Enhancers	Dnd41	blood

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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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