Variant report

Variant	rs11003452
Chromosome Location	chr10:54968258-54968259
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10824936	0.94[ASN][1000 genomes]
rs10824937	0.96[ASN][1000 genomes]
rs10824947	0.99[ASN][1000 genomes]
rs10824949	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10824952	0.92[ASN][1000 genomes]
rs11003448	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11003456	0.99[ASN][1000 genomes]
rs11003457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11003459	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11003469	0.96[ASN][1000 genomes]
rs11003470	0.96[ASN][1000 genomes]
rs11003475	0.92[ASN][1000 genomes]
rs12763554	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16937295	0.92[ASN][1000 genomes]
rs1903948	0.92[ASN][1000 genomes]
rs1904055	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947757	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993855	0.99[ASN][1000 genomes]
rs1993856	0.99[ASN][1000 genomes]
rs2384161	0.99[ASN][1000 genomes]
rs2384162	0.99[ASN][1000 genomes]
rs2384163	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2384164	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2891440	0.94[ASN][1000 genomes]
rs4427482	0.96[ASN][1000 genomes]
rs4935063	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935064	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935068	0.92[ASN][1000 genomes]
rs4935400	0.96[ASN][1000 genomes]
rs4935405	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7893316	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752952	chr10:54900994-55497594	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv831878	chr10:54902106-55085586	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1054455	chr10:54932474-55001559	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
4	nsv895408	chr10:54938398-54999514	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11003452	GFPT1	trans	parietal	SCAN
rs11003452	PRKG1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54966000-54969600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr10:54966400-54981600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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