Variant report

Variant	rs7041489
Chromosome Location	chr9:3177813-3177814
allele	C/T
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	USF1	chr9:3177652-3177984	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF12	chr9:3177747-3177923	H1-hESC	embryonic stem cell:	n/a	n/a
3	FOXA2	chr9:3177069-3178002	HepG2	liver:	n/a	n/a
4	FOXA1	chr9:3177243-3177827	HepG2	liver:	n/a	n/a
5	USF1	chr9:3177613-3177960	H1-hESC	embryonic stem cell:	n/a	n/a
6	HNF4G	chr9:3177303-3177826	HepG2	liver:	n/a	n/a
7	MYBL2	chr9:3177284-3177861	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000236511	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10813628	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10813629	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10970482	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1885471	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7024687	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7038505	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7862467	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7869695	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892085	chr9:2937654-3215842	Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1017474	chr9:3019068-3247215	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv892088	chr9:3019383-3215842	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1028668	chr9:3139007-3262791	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv539939	chr9:3139007-3262791	Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3174400-3178200	Enhancers	Primary hematopoietic stem cells	blood
2	chr9:3175400-3178200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr9:3175400-3178200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr9:3176400-3178200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:3176400-3178200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:3176800-3178400	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr9:3176800-3178600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr9:3177200-3178000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:3177200-3178400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr9:3177200-3179600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:3177400-3178000	Enhancers	Adipose Nuclei	Adipose
12	chr9:3177400-3178200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr9:3177400-3178600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:3177400-3178600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:3177600-3178000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr9:3177600-3181000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:3177800-3178000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr9:3177800-3178000	Enhancers	H9 Cell Line	embryonic stem cell
19	chr9:3177800-3178000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:3177800-3178000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:3177800-3178600	Enhancers	HepG2	liver
22	chr9:3177800-3178600	Enhancers	NHDF-Ad	bronchial
23	chr9:3177800-3179800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:3177800-3181000	Weak transcription	Pancreas	Pancrea

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