Variant report

Variant	rs2518493
Chromosome Location	chr1:158631171-158631172
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1029083	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2022002	0.85[EUR][1000 genomes]
rs2157691	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs2246434	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2251963	0.84[EUR][1000 genomes]
rs2251964	0.84[EUR][1000 genomes]
rs2479868	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs2482963	0.84[EUR][1000 genomes]
rs2518489	0.84[EUR][1000 genomes]
rs2518490	0.84[EUR][1000 genomes]
rs2518491	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2779116	0.85[EUR][1000 genomes]
rs2852634	0.85[EUR][1000 genomes]
rs2852635	0.85[EUR][1000 genomes]
rs2852637	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703118	0.94[JPT][hapmap]
rs703127	0.88[JPT][hapmap]
rs751258	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs857684	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs857685	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs857689	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs857691	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs857720	0.82[EUR][1000 genomes]
rs857721	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs857725	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs857938	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs857940	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs860772	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs861409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs863327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	esv3491788	chr1:158537183-158725907	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv3491789	chr1:158537242-158725858	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv872481	chr1:158625789-158712510	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2518493	CHRNB2	cis	cerebellum	SCAN
rs2518493	PYHIN1	cis	cerebellum	SCAN
rs2518493	SLC27A3	cis	cerebellum	SCAN
rs2518493	IFI16	cis	parietal	SCAN
rs2518493	OR6Y1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158629800-158633600	Strong transcription	K562	blood
2	chr1:158631000-158631200	Enhancers	Pancreas	Pancrea

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