Variant report

Variant	rs158990
Chromosome Location	chr5:57972853-57972854
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1035393	0.85[ASN][1000 genomes]
rs1422226	0.85[ASN][1000 genomes]
rs149351	0.87[ASN][1000 genomes]
rs149525	0.87[ASN][1000 genomes]
rs158955	0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs158957	0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs158958	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs158970	0.88[GIH][hapmap]
rs158974	0.86[GIH][hapmap]
rs158977	0.86[GIH][hapmap]
rs158980	0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap]
rs158987	0.86[ASN][1000 genomes]
rs158993	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs158997	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs158999	0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs159000	0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs159002	0.88[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap]
rs159003	0.89[ASN][1000 genomes]
rs159004	0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs159006	0.89[ASN][1000 genomes]
rs159007	0.85[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs159008	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs169705	0.86[GIH][hapmap]
rs176637	0.87[ASN][1000 genomes]
rs176807	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs186010	0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1895232	0.90[CHB][hapmap];0.83[YRI][hapmap];0.85[ASN][1000 genomes]
rs2032815	0.94[CEU][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2161246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591922	0.85[ASN][1000 genomes]
rs2591924	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs290572	0.95[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs292984	0.86[GIH][hapmap]
rs292985	0.86[GIH][hapmap]
rs293005	0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[ASN][1000 genomes]
rs293006	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs293007	0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs293008	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs293009	0.80[CHB][hapmap];0.80[ASN][1000 genomes]
rs293018	0.90[CHB][hapmap];0.84[CHD][hapmap];0.87[YRI][hapmap];0.85[ASN][1000 genomes]
rs293019	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs293023	0.93[ASN][1000 genomes]
rs293025	0.90[CHB][hapmap];0.84[CHD][hapmap];0.85[ASN][1000 genomes]
rs293026	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs293027	0.85[ASN][1000 genomes]
rs293029	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs380850	0.86[GIH][hapmap]
rs49961	0.85[ASN][1000 genomes]
rs63710	0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9790998	0.80[JPT][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	nsv4845	chr5:57949493-57994156	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs158990	KIF2A	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57967400-57973600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:57967400-57977800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:57971800-57978400	Enhancers	HUVEC	blood vessel
4	chr5:57972800-57973000	Enhancers	Spleen	Spleen
5	chr5:57972800-57973200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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