Variant report

Variant	rs17533116
Chromosome Location	chr15:45588758-45588759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10152337	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10152697	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12324848	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1288861	0.81[CEU][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs16940351	0.81[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs16941238	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs16942066	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1706799	0.91[CEU][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs17533716	0.84[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17535381	1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17537244	1.00[JPT][hapmap]
rs17618294	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2433229	0.83[JPT][hapmap]
rs2433602	0.83[EUR][1000 genomes]
rs2453546	0.80[EUR][1000 genomes]
rs2461706	0.83[EUR][1000 genomes]
rs2486287	0.84[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2668746	0.91[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs55721266	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55904415	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56267974	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56306977	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57369693	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57419781	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57805764	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs61301536	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72709081	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72709084	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72709088	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72711253	0.82[EUR][1000 genomes]
rs72711255	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9972405	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9972498	0.82[ASW][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9972528	0.81[AMR][1000 genomes];0.86[EUR][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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17533116	SLC28A2	cis	cerebellum	SCAN
rs17533116	ITPKA	cis	cerebellum	SCAN
rs17533116	SLC30A4	cis	parietal	SCAN
rs17533116	MGA	cis	parietal	SCAN
rs17533116	SPATA5L1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45572200-45592000	Weak transcription	Right Atrium	heart

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