Variant report

Variant	rs17045065
Chromosome Location	chr2:53877551-53877552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10490465	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11900355	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17045037	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17045048	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17045081	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17045084	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34408637	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3731970	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs3770407	0.82[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs3770408	0.86[EUR][1000 genomes]
rs3770411	0.85[CEU][hapmap];0.91[LWK][hapmap]
rs3930	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4525731	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56056250	0.97[ASN][1000 genomes]
rs56081218	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56383522	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58125503	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58515086	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62139773	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62139774	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62139775	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62139785	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62139836	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72901209	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7583622	0.88[ASW][hapmap];0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv874147	chr2:53772561-53886799	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17045065	PSME4	cis	cerebellum	SCAN
rs17045065	RBM33	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea

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