Variant report

Variant	rs7254188
Chromosome Location	chr19:41407343-41407344
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10406188	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10410750	0.88[ASN][1000 genomes]
rs10411264	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10411877	0.86[ASN][1000 genomes]
rs10414481	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10416968	0.98[ASN][1000 genomes]
rs10418318	0.93[ASN][1000 genomes]
rs10419393	0.95[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10421888	0.92[ASN][1000 genomes]
rs10423165	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10424834	0.81[ASN][1000 genomes]
rs10425176	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs11083577	0.83[ASN][1000 genomes]
rs11083580	0.86[ASN][1000 genomes]
rs11083582	0.93[ASN][1000 genomes]
rs11665969	0.92[ASN][1000 genomes]
rs12973598	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12975382	0.81[ASN][1000 genomes]
rs12982395	0.88[ASN][1000 genomes]
rs2316213	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2644904	0.85[ASN][1000 genomes]
rs28472879	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28503746	0.91[ASN][1000 genomes]
rs28619553	0.88[ASN][1000 genomes]
rs2935235	0.87[ASN][1000 genomes]
rs3797218	0.88[ASN][1000 genomes]
rs3815714	0.86[ASN][1000 genomes]
rs3852870	0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3865457	0.84[JPT][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3869579	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3875159	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs3909341	0.92[ASN][1000 genomes]
rs3909342	0.93[ASN][1000 genomes]
rs4105141	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4105142	0.92[ASN][1000 genomes]
rs4105143	0.90[ASN][1000 genomes]
rs4142867	0.88[ASN][1000 genomes]
rs4802095	0.81[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs4803389	0.88[ASN][1000 genomes]
rs4803390	0.85[ASN][1000 genomes]
rs4803391	0.87[ASN][1000 genomes]
rs4803393	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4803400	0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs5007415	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56081734	0.88[ASN][1000 genomes]
rs61482096	0.83[ASN][1000 genomes]
rs6508953	0.87[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs67421541	0.93[ASN][1000 genomes]
rs7252852	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7258590	0.87[ASN][1000 genomes]
rs7258728	0.93[ASN][1000 genomes]
rs7343061	0.96[ASN][1000 genomes]
rs8103288	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1066637	chr19:41309211-41597896	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv3337314	chr19:41388910-41534583	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv960838	chr19:41401531-41413740	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7254188	NANOS2	cis	parietal	SCAN
rs7254188	LYPD4	cis	cerebellum	SCAN
rs7254188	CABP5	cis	cerebellum	SCAN
rs7254188	ZNF541	cis	cerebellum	SCAN
rs7254188	PRKD2	cis	parietal	SCAN
rs7254188	RELB	cis	parietal	SCAN
rs7254188	KPTN	cis	parietal	SCAN
rs7254188	SLC17A7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41403000-41414200	Weak transcription	Lung	lung
2	chr19:41406800-41410400	Weak transcription	K562	blood

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