Variant report

Variant	rs4557559
Chromosome Location	chr6:118406802-118406803
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs4276535	0.81[ASW][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap]
rs4412242	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4587199	0.83[YRI][hapmap]
rs4946324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73766414	0.86[EUR][1000 genomes]
rs9385033	0.86[YRI][hapmap];0.96[AFR][1000 genomes]
rs9385034	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs9401057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4557559	OLIG3	trans	brain	seeQTL
rs4557559	USH1G	trans	brain	seeQTL
rs4557559	MLLT1	trans	brain	seeQTL
rs4557559	SIPA1L3	trans	brain	seeQTL
rs4557559	IDO2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118377200-118408600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:118386600-118409600	Weak transcription	Cortex derived primary cultured neurospheres	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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