Variant report

Variant	rs2070895
Chromosome Location	chr15:58723939-58723940
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	RXRA	chr15:58723718-58724069	HepG2	liver:	n/a	chr15:58723958-58723972 chr15:58723957-58723966
2	CEBPB	chr15:58723779-58724009	HepG2	liver:	n/a	chr15:58723909-58723921
3	USF1	chr15:58723730-58723975	HepG2	liver:	n/a	n/a
4	MAX	chr15:58723706-58724028	HepG2	liver:	n/a	chr15:58723874-58723884
5	EP300	chr15:58723407-58724097	HepG2	liver:	n/a	chr15:58723600-58723610
6	HDAC2	chr15:58723605-58724109	HepG2	liver:	n/a	chr15:58723782-58723796
7	MAX	chr15:58723612-58724127	HepG2	liver:	n/a	chr15:58723874-58723884
8	FOXA2	chr15:58723752-58723994	HepG2	liver:	n/a	n/a
9	FOXA1	chr15:58723346-58724175	HepG2	liver:	n/a	n/a
10	SIN3AK20	chr15:58723748-58723950	HepG2	liver:	n/a	n/a
11	MAX	chr15:58723517-58724697	HepG2	liver:	n/a	chr15:58723874-58723884
12	ARID3A	chr15:58723845-58724674	HepG2	liver:	n/a	n/a
13	MXI1	chr15:58723548-58724555	HepG2	liver:	n/a	chr15:58723874-58723883
14	FOXA1	chr15:58723321-58724076	HepG2	liver:	n/a	n/a
15	HNF4G	chr15:58723731-58724052	HepG2	liver:	n/a	chr15:58723951-58723964 chr15:58723958-58723971 chr15:58723951-58723964 chr15:58723958-58723970
16	MYC	chr15:58723701-58724072	HepG2	liver:	n/a	chr15:58723874-58723884
17	FOXA1	chr15:58723364-58724031	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
LIPC	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1077834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800588	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs261332	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs261334	0.91[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs261342	0.86[CEU][hapmap]
rs588136	0.90[CEU][hapmap];0.81[CHB][hapmap];0.87[EUR][1000 genomes]
rs8033940	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529717	chr15:58519923-58756814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1042201	chr15:58520746-58780710	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv904267	chr15:58699010-58769583	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1047048	chr15:58701400-58784800	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2760372	chr15:58721447-58731153	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Blood metabolite levels	24816252	GWAS catalog

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58704600-58728800	Weak transcription	Thymus	Thymus
2	chr15:58716600-58725800	Weak transcription	Right Atrium	heart
3	chr15:58716600-58726600	Weak transcription	Esophagus	oesophagus
4	chr15:58717800-58724400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:58718000-58724600	Weak transcription	NHDF-Ad	bronchial
6	chr15:58718400-58726600	Weak transcription	Stomach Mucosa	stomach
7	chr15:58718600-58725000	Weak transcription	Fetal Lung	lung
8	chr15:58719600-58725800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:58722000-58724400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:58722600-58724200	Weak transcription	Right Ventricle	heart
11	chr15:58722600-58731000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:58723400-58724000	Flanking Active TSS	HepG2	liver
13	chr15:58723400-58724200	Enhancers	A549	lung
14	chr15:58723400-58724400	Enhancers	Fetal Kidney	kidney
15	chr15:58723600-58724000	Enhancers	Pancreas	Pancrea
16	chr15:58723600-58724200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:58723600-58724200	Enhancers	Hela-S3	cervix
18	chr15:58723600-58724400	Enhancers	Fetal Thymus	thymus
19	chr15:58723600-58724600	Enhancers	Duodenum Mucosa	Duodenum
20	chr15:58723600-58725000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:58723600-58725000	Enhancers	Fetal Intestine Large	intestine
22	chr15:58723800-58724000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:58723800-58724000	Enhancers	Liver	Liver
24	chr15:58723800-58724400	Enhancers	Fetal Intestine Small	intestine
25	chr15:58723800-58724400	Weak transcription	K562	blood

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