Variant report

Variant	rs241944
Chromosome Location	chr19:38302583-38302584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10422056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11083438	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665877	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11668384	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668434	0.82[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes]
rs11668558	1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes]
rs11672077	0.82[ASW][hapmap];0.89[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12462485	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610891	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972712	0.92[AMR][1000 genomes]
rs12981237	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12982288	0.83[AMR][1000 genomes]
rs1643470	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs1643472	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1725490	0.82[EUR][1000 genomes]
rs17306508	0.82[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes]
rs17306795	0.89[CHB][hapmap]
rs1871197	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2160640	0.82[ASW][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap]
rs241937	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241946	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241947	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241948	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs241951	0.89[CHB][hapmap];0.91[CHD][hapmap]
rs241953	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs241957	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs241959	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs241960	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972456	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2972459	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs34607899	0.92[AMR][1000 genomes]
rs34782935	0.83[AMR][1000 genomes]
rs34949193	0.86[AMR][1000 genomes]
rs35015599	0.92[AMR][1000 genomes]
rs35214625	0.92[AMR][1000 genomes]
rs353405	0.81[EUR][1000 genomes]
rs353406	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs353409	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs353412	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs353413	0.84[EUR][1000 genomes]
rs35415221	0.83[AMR][1000 genomes]
rs36020184	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs36092052	0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3752365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes]
rs3894129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4482404	0.82[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes]
rs4802134	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803536	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803566	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57308437	0.83[AMR][1000 genomes]
rs62108339	0.83[AMR][1000 genomes]
rs62108355	0.85[AMR][1000 genomes]
rs6508748	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508752	0.86[EUR][1000 genomes]
rs697433	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7250668	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254170	0.82[ASW][hapmap];0.89[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap]
rs7254828	1.00[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7255551	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8102871	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8103882	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105694	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110417	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8111400	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs833916	1.00[CHB][hapmap]
rs856302	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs856309	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs861308	1.00[CHB][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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs241944	ARHGEF1	cis	cerebellum	SCAN
rs241944	TMEM145	cis	parietal	SCAN
rs241944	GSK3A	cis	parietal	SCAN
rs241944	CD3EAP	cis	cerebellum	SCAN
rs241944	PPP5C	cis	parietal	SCAN
rs241944	ITPKC	cis	cerebellum	SCAN
rs241944	CEACAM16	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38299200-38304000	Weak transcription	Colon Smooth Muscle	Colon
2	chr19:38302400-38303000	ZNF genes & repeats	Aorta	Aorta

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