Variant report

Variant	rs158970
Chromosome Location	chr5:57943627-57943628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1019469	0.85[JPT][hapmap]
rs1035394	0.81[JPT][hapmap]
rs158955	0.93[GIH][hapmap]
rs158957	0.93[GIH][hapmap]
rs158964	0.80[MEX][hapmap];0.84[YRI][hapmap]
rs158965	0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs158968	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs158972	0.85[EUR][1000 genomes]
rs158973	0.85[EUR][1000 genomes]
rs158974	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]
rs158977	0.92[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes]
rs158979	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs158990	0.88[GIH][hapmap]
rs169705	0.92[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.85[EUR][1000 genomes]
rs17346755	0.84[JPT][hapmap];0.88[MEX][hapmap]
rs2032815	0.90[GIH][hapmap]
rs2161246	0.83[GIH][hapmap]
rs2545791	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2591914	0.95[JPT][hapmap];0.91[YRI][hapmap];0.87[ASN][1000 genomes]
rs292970	0.82[ASW][hapmap];0.91[CEU][hapmap];0.80[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs292971	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs292981	0.85[EUR][1000 genomes]
rs292982	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs292983	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs292984	0.92[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs292985	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[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]
rs292986	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs292987	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs292992	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377601	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs377695	0.82[EUR][1000 genomes]
rs380850	0.92[CEU][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs389543	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs393390	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs393400	1.00[CEU][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs394979	0.82[EUR][1000 genomes]
rs404701	0.82[EUR][1000 genomes]
rs413605	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs423522	0.82[EUR][1000 genomes]
rs430261	0.82[EUR][1000 genomes]
rs430587	0.82[EUR][1000 genomes]
rs430763	0.82[EUR][1000 genomes]
rs433188	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs434759	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs435514	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs441085	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs442414	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs444108	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs449804	0.82[EUR][1000 genomes]
rs449867	1.00[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs452321	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs63710	0.93[GIH][hapmap]
rs965795	0.81[JPT][hapmap]
rs984664	0.82[ASW][hapmap];0.82[YRI][hapmap]

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	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
4	nsv1020937	chr5:57938969-57959918	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs158970	KIF2A	cis	cerebellum	SCAN
rs158970	C5orf43	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57933600-57944000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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