Variant report

Variant	rs3909341
Chromosome Location	chr19:41393326-41393327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr19:41392657-41393343	A549	lung:	n/a	chr19:41392870-41392884
2	NR3C1	chr19:41392618-41393362	A549	lung:	n/a	chr19:41392870-41392884

Variant related genes	Relation type
CYP2G1P	TF binding region
CYP2A7	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10406188	0.97[ASN][1000 genomes]
rs10410750	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10411264	0.97[ASN][1000 genomes]
rs10411877	0.84[ASN][1000 genomes]
rs10414481	0.97[ASN][1000 genomes]
rs10416968	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10418318	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10419393	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10421888	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423165	0.93[ASN][1000 genomes]
rs10424691	0.84[ASN][1000 genomes]
rs10424834	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10425037	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11083577	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11083580	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083582	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11665969	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669113	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12973598	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12975382	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12982395	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2316215	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644904	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28427254	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28472879	0.97[ASN][1000 genomes]
rs28503746	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28619553	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2935235	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797218	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815714	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3852870	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3865457	0.96[ASN][1000 genomes]
rs3869579	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3875159	0.80[ASN][1000 genomes]
rs3909342	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4105141	0.97[ASN][1000 genomes]
rs4105142	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4105143	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4142867	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802095	0.92[ASN][1000 genomes]
rs4803389	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803390	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803391	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803400	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5007415	0.97[ASN][1000 genomes]
rs56081734	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61482096	0.89[ASN][1000 genomes]
rs6508953	0.90[ASN][1000 genomes]
rs67421541	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7252852	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254188	0.92[ASN][1000 genomes]
rs7258590	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7258728	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7343061	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8103288	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv2760509	chr19:41325004-41394336	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1056244	chr19:41329218-41397661	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv1827726	chr19:41329872-41395056	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv1832156	chr19:41332004-41399077	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv9729	chr19:41337805-41394407	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1065886	chr19:41339857-41397661	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv33053	chr19:41340629-41400635	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv1827139	chr19:41348820-41395889	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv579549	chr19:41354629-41393760	Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv579556	chr19:41355999-41393760	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv1056284	chr19:41360131-41399887	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	nsv1055263	chr19:41360358-41397661	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3909341	CYP2G1P	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41392600-41394000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:41392800-41394400	Enhancers	A549	lung
3	chr19:41393200-41394200	Weak transcription	Adipose Nuclei	Adipose
4	chr19:41393200-41397600	Weak transcription	Ovary	ovary

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