Variant report

Variant	rs5982340
Chromosome Location	chrX:76230687-76230688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 5 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs5938805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs958410	1.00[CEU][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.93[MEX][hapmap]

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	esv2830377	chrX:75525310-76337197	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv498037	chrX:75586665-76291236	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	esv3347407	chrX:75769946-76251749	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs5982340	LRTOMT	trans	brain	seeQTL
rs5982340	ACSBG1	trans	brain	seeQTL
rs5982340	NR1H3	trans	brain	seeQTL
rs5982340	BCL6B	trans	brain	seeQTL
rs5982340	TNFSF12-TNFSF13	trans	brain	seeQTL
rs5982340	CABLES1	trans	brain	seeQTL
rs5982340	C20orf72	trans	brain	seeQTL
rs5982340	TBC1D16	trans	brain	seeQTL
rs5982340	RXRG	trans	brain	seeQTL
rs5982340	GPR143	trans	brain	seeQTL
rs5982340	DARS2	trans	brain	seeQTL
rs5982340	EHD2	trans	brain	seeQTL
rs5982340	IMPA2	trans	brain	seeQTL
rs5982340	CYP11A1	trans	brain	seeQTL
rs5982340	DNAH7	trans	brain	seeQTL
rs5982340	MSI2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chrX:76219800-76232200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chrX:76230400-76230800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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