Variant report

Variant	rs9551590
Chromosome Location	chr13:29589465-29589466
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1358937	0.95[ASN][1000 genomes]
rs1407438	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[ASN][1000 genomes]
rs226904	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs226905	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs226909	1.00[MEX][hapmap]
rs2475539	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs2475540	0.98[ASN][1000 genomes]
rs2475541	0.98[ASN][1000 genomes]
rs2475542	0.98[ASN][1000 genomes]
rs2475543	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2479759	0.98[ASN][1000 genomes]
rs2479760	0.98[ASN][1000 genomes]
rs2479764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2479765	0.98[ASN][1000 genomes]
rs2479766	0.98[ASN][1000 genomes]
rs2479767	0.98[ASN][1000 genomes]
rs2479768	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.98[ASN][1000 genomes]
rs2484464	0.98[ASN][1000 genomes]
rs2484465	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs2484466	0.98[ASN][1000 genomes]
rs28434554	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2987343	0.98[ASN][1000 genomes]
rs2987346	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[TSI][hapmap];0.98[ASN][1000 genomes]
rs326509	1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs326510	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs326511	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs4238114	1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4769660	1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4769669	0.98[ASN][1000 genomes]
rs60782582	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7318626	0.98[ASN][1000 genomes]
rs74041703	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs74045518	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984343	1.00[ASN][1000 genomes]
rs9506076	1.00[CHB][hapmap]
rs9550433	0.98[ASN][1000 genomes]
rs9550434	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs9551587	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9551588	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9551589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9551591	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9551592	0.98[ASN][1000 genomes]
rs9578069	0.83[ASN][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	nsv533835	chr13:29141132-29962069	Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs9551590	LTBP2	trans	brain	seeQTL
rs9551590	LRRN4CL	trans	brain	seeQTL
rs9551590	SLC26A2	trans	brain	seeQTL
rs9551590	PDGFRL	trans	brain	seeQTL
rs9551590	KLF5	trans	brain	seeQTL
rs9551590	SFRP2	trans	brain	seeQTL
rs9551590	BMP5	trans	brain	seeQTL
rs9551590	UPK1B	trans	brain	seeQTL
rs9551590	OMD	trans	brain	seeQTL
rs9551590	KLK1	trans	brain	seeQTL
rs9551590	PTGDR	trans	brain	seeQTL
rs9551590	ITGBL1	trans	brain	seeQTL
rs9551590	FGL2	trans	brain	seeQTL
rs9551590	TNFRSF11B	trans	brain	seeQTL
rs9551590	FAT4	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:29585000-29609600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:29588800-29589800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr13:29589400-29589600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr13:29589400-29589600	Enhancers	Fetal Heart	heart
5	chr13:29589400-29599000	Weak transcription	Aorta	Aorta

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