Variant report

Variant	rs17074894
Chromosome Location	chr3:42967174-42967175
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10470680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129987	0.83[EUR][1000 genomes]
rs11129988	0.83[EUR][1000 genomes]
rs123506	1.00[CHB][hapmap]
rs12629332	1.00[CHB][hapmap]
rs1392319	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1403525	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17238972	1.00[ASN][1000 genomes]
rs1816227	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28378297	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601753	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655956	1.00[ASN][1000 genomes]
rs28673478	1.00[ASN][1000 genomes]
rs339682	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs339683	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs339686	1.00[CHB][hapmap]
rs3915020	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4404423	1.00[CHB][hapmap]
rs489117	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs526511	0.82[EUR][1000 genomes]
rs530842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs534284	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs542394	0.82[EUR][1000 genomes]
rs545023	0.82[EUR][1000 genomes]
rs551658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604393	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs60616619	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61004728	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615462	0.80[EUR][1000 genomes]
rs617014	1.00[ASN][1000 genomes]
rs619660	0.81[EUR][1000 genomes]
rs62248962	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249006	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249007	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249008	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249009	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249011	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249013	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249014	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249015	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62249016	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249584	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638602	0.82[EUR][1000 genomes]
rs649682	0.82[EUR][1000 genomes]
rs651899	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6763762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773223	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775999	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782601	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs678310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6798412	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798520	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs680967	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs681341	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs73075297	1.00[ASN][1000 genomes]
rs73075301	1.00[ASN][1000 genomes]
rs73077208	1.00[ASN][1000 genomes]
rs73077214	1.00[ASN][1000 genomes]
rs73077238	1.00[ASN][1000 genomes]
rs73087348	1.00[ASN][1000 genomes]
rs735320	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs73832423	1.00[ASN][1000 genomes]
rs73832424	1.00[ASN][1000 genomes]
rs7617715	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625959	0.94[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs7641452	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644923	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs834183	0.82[EUR][1000 genomes]
rs834579	1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs834584	1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs834699	0.82[EUR][1000 genomes]
rs9311330	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815609	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9816391	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9824700	1.00[ASN][1000 genomes]
rs9828785	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs9832875	1.00[ASW][hapmap];0.95[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9833284	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837761	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840349	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9852930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858270	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862469	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9865715	1.00[CHB][hapmap]
rs9870478	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv3783	chr3:42926223-42970597	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17074894	KIF15	cis	parietal	SCAN
rs17074894	HHATL	cis	cerebellum	SCAN
rs17074894	HIGD1A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42962400-42980400	Weak transcription	Placenta	Placenta
2	chr3:42967000-42967200	Enhancers	Stomach Smooth Muscle	stomach

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