Variant report

Variant	rs17164457
Chromosome Location	chr5:116809926-116809927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1428046	0.91[ASN][1000 genomes]
rs2081859	1.00[ASN][1000 genomes]
rs2099039	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560503	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2560507	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2560513	0.93[ASN][1000 genomes]
rs2560514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2560518	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2560634	1.00[ASN][1000 genomes]
rs2560636	0.99[ASN][1000 genomes]
rs2560637	0.99[ASN][1000 genomes]
rs2624506	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2624514	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2624569	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs2624570	0.86[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs970350	1.00[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830457	chr5:116724777-116875060	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv882756	chr5:116783660-116905052	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17164457	SEMA6A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:116808600-116810000	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr5:116809000-116810000	Enhancers	Brain Germinal Matrix	brain

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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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