Variant report

Variant	rs158974
Chromosome Location	chr5:57928518-57928519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs158955	0.90[GIH][hapmap]
rs158957	0.90[GIH][hapmap]
rs158964	0.81[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.84[YRI][hapmap]
rs158965	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs158968	0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs158969	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs158970	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs158972	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158973	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs158977	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs158979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs158990	0.86[GIH][hapmap]
rs169705	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17346755	0.88[MEX][hapmap]
rs2032815	0.88[GIH][hapmap]
rs2161246	0.81[GIH][hapmap]
rs2545791	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2591914	0.91[YRI][hapmap]
rs292970	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs292971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs292981	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292983	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292984	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs292985	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292986	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292987	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs292992	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs377601	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs377695	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380850	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs389543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393390	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs394979	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs404701	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs413605	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs423522	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs430261	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs430587	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs430763	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs433188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs441085	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs442414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444108	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs449804	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs452321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700302	0.86[JPT][hapmap]
rs63710	0.90[GIH][hapmap]
rs984664	1.00[ASW][hapmap];0.82[YRI][hapmap]

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	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1029145	chr5:57905821-58141221	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830311	chr5:57912546-58105636	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs158974	KIF2A	cis	cerebellum	SCAN
rs158974	ANKRD28	trans	brain	seeQTL
rs158974	C5orf43	cis	parietal	SCAN
rs158974	KIAA0379	trans	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57921000-57933000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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