Variant report

Variant	rs62539265
Chromosome Location	chr9:44110749-44110750
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	BATF	chr9:44110695-44110955	GM12878	blood:	n/a	n/a
2	BCL11A	chr9:44110718-44110942	GM12878	blood:	n/a	n/a
3	RXRA	chr9:44110627-44110981	HepG2	liver:	n/a	chr9:44110746-44110760
4	IRF4	chr9:44110625-44110971	GM12878	blood:	n/a	n/a
5	EP300	chr9:44110625-44110952	GM12878	blood:	n/a	n/a
6	BCL11A	chr9:44110687-44111019	GM12878	blood:	n/a	n/a
7	SP1	chr9:44110693-44110964	GM12878	blood:	n/a	n/a
8	PAX5	chr9:44110689-44110891	GM12878	blood:	n/a	n/a
9	POU2F2	chr9:44110610-44111009	GM12878	blood:	n/a	chr9:44110972-44110987 chr9:44110966-44110981 chr9:44110616-44110629 chr9:44110694-44110708
10	FOXA1	chr9:44110602-44111055	HepG2	liver:	n/a	chr9:44111029-44111041
11	JUND	chr9:44110682-44110950	HepG2	liver:	n/a	chr9:44110692-44110701
12	BATF	chr9:44110679-44110958	GM12878	blood:	n/a	n/a
13	TCF12	chr9:44110707-44110900	HepG2	liver:	n/a	n/a
14	FOXA1	chr9:44110544-44110872	HepG2	liver:	n/a	n/a
15	EP300	chr9:44110648-44110858	HepG2	liver:	n/a	n/a
16	SP1	chr9:44110569-44111034	HepG2	liver:	n/a	n/a
17	CTCF	chr9:44110699-44110763	Kidney_OC	kidney:	n/a	n/a
18	RXRA	chr9:44110623-44110928	HepG2	liver:	n/a	chr9:44110746-44110760
19	TCF12	chr9:44110678-44110943	GM12878	blood:	n/a	n/a
20	FOXA2	chr9:44110589-44110829	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
RNU6-599P	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs28395168	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28449753	0.80[ASN][1000 genomes]
rs28532674	0.82[ASN][1000 genomes]
rs28576093	0.80[ASN][1000 genomes]
rs28588544	0.87[ASN][1000 genomes]
rs28612439	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28651802	0.86[AMR][1000 genomes]
rs28685579	0.80[ASN][1000 genomes]
rs28707204	0.86[ASN][1000 genomes]
rs28820585	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3890449	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62538286	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62538297	0.92[AMR][1000 genomes]
rs62538300	0.91[AMR][1000 genomes]
rs62538301	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62538306	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62538308	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62538315	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62538321	0.80[AMR][1000 genomes]
rs62539263	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62539264	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62539269	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67169668	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:37 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv436621	chr9:43145796-44122367	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1030874	chr9:43315962-44114860	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1021270	chr9:43315962-44145340	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1024462	chr9:43315962-44205637	Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1029200	chr9:43437359-44214733	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1015727	chr9:43505840-44114860	Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1025269	chr9:43505840-44136778	Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv1029217	chr9:43505840-44145340	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1027371	chr9:43505840-44273229	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1032592	chr9:43505840-44396915	ZNF genes & repeats Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1021421	chr9:43505840-44469316	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	esv2753911	chr9:43530395-44466984	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	esv2756103	chr9:43530395-44466984	Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv1015636	chr9:43612150-44145340	ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Strong transcription	TF binding region CpG island lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1029109	chr9:43612150-44273229	ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
16	nsv1026029	chr9:43612150-44446124	Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	nsv1029916	chr9:43612150-44466205	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
18	nsv1034880	chr9:43612150-44469316	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
19	nsv1016609	chr9:43654127-44241805	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv1016330	chr9:43654127-44273229	Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
21	nsv1030605	chr9:43654127-44469316	Bivalent Enhancer Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
22	nsv1019786	chr9:43675599-44469316	Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
23	nsv1024443	chr9:43700866-44469316	Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
24	nsv1020552	chr9:43726990-44273229	Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
25	nsv1018992	chr9:43726990-44469316	Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
26	nsv1015988	chr9:43734207-44469316	Bivalent Enhancer ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
27	nsv1034869	chr9:43757334-44739032	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
28	nsv1018198	chr9:43772038-44469316	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
29	nsv1026263	chr9:43776906-44469316	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
30	nsv1029361	chr9:43800174-44273229	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
31	esv1828893	chr9:43936609-44463095	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
32	esv1822441	chr9:43941952-44475321	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
33	nsv968643	chr9:43997036-44139152	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island lncRNA	8 gene(s)	inside rSNPs	diseases
34	esv1821075	chr9:44015421-44475321	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
35	esv1833488	chr9:44046700-44821943	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
36	esv9914	chr9:44071111-44115070	Weak transcription Enhancers Strong transcription	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
37	nsv973634	chr9:44101518-44113586	Weak transcription Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs62539265	CR848007.2	cis	Nerve Tibial	GTEx
rs62539265	CR848007.2	cis	Thyroid	GTEx
rs62539265	ANKRD20A7P	cis	Artery Tibial	GTEx
rs62539265	ANKRD20A7P	cis	Skin Sun Exposed Lower leg	GTEx
rs62539265	ANKRD20A7P	cis	Nerve Tibial	GTEx
rs62539265	ANKRD20A7P	cis	Adipose Subcutaneous	GTEx
rs62539265	ANKRD20A7P	cis	Esophagus Muscularis	GTEx
rs62539265	CR848007.2	cis	Adipose Subcutaneous	GTEx
rs62539265	ANKRD20A7P	cis	Thyroid	GTEx
rs62539265	ANKRD20A7P	cis	Heart Left Ventricle	GTEx
rs62539265	ANKRD20A7P	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:44109600-44111200	Weak transcription	HepG2	liver
2	chr9:44110200-44112000	Weak transcription	Liver	Liver

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