Variant report

Variant	rs17140
Chromosome Location	chr3:54565908-54565909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11130423	0.89[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11707007	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11708915	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11711518	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11713519	0.92[ASN][1000 genomes]
rs11714447	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs13073425	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13089488	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17747001	0.81[JPT][hapmap]
rs2053862	0.89[CEU][hapmap]
rs28507696	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2884804	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs57828037	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58452494	0.91[EUR][1000 genomes]
rs6414584	0.96[CEU][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6445673	0.89[CEU][hapmap]
rs6445677	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs6445680	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6445682	0.96[CEU][hapmap]
rs6445684	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6445685	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs6445687	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs6445690	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6775352	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6789926	1.00[CEU][hapmap]
rs6790503	0.96[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs6795380	0.96[CEU][hapmap]
rs6798952	0.96[CEU][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs7372541	0.84[CEU][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs7372624	0.91[EUR][1000 genomes]
rs7374204	0.85[CEU][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs7428361	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7431090	0.91[EUR][1000 genomes]
rs7432776	0.86[CHD][hapmap]
rs7432845	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs7636708	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs9816842	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9874147	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9874177	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv876810	chr3:54480798-54585416	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17140	HEMK1	cis	cerebellum	SCAN
rs17140	DNASE1L3	cis	parietal	SCAN
rs17140	MAPKAPK3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54564000-54566400	Enhancers	Psoas Muscle	Psoas
2	chr3:54564800-54566000	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr3:54565200-54566400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:54565600-54566200	Enhancers	Skeletal Muscle Female	skeletal muscle

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