Variant report

Variant	rs12554342
Chromosome Location	chr9:116840801-116840802
allele	C/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	RCOR1	chr9:116840744-116841027	K562	blood:	n/a	n/a
2	RAD21	chr9:116840408-116840954	HepG2	liver:	n/a	n/a
3	TCF12	chr9:116840415-116840951	HepG2	liver:	n/a	n/a
4	JUND	chr9:116840375-116840973	HepG2	liver:	n/a	chr9:116840839-116840850
5	MXI1	chr9:116840018-116841106	HepG2	liver:	n/a	n/a
6	MAZ	chr9:116840453-116841011	HepG2	liver:	n/a	n/a
7	JUND	chr9:116840534-116841012	HepG2	liver:	n/a	chr9:116840839-116840850
8	CEBPD	chr9:116840273-116840979	HepG2	liver:	n/a	n/a
9	YY1	chr9:116840629-116840944	H1-hESC	embryonic stem cell:	n/a	n/a
10	FOXA1	chr9:116840322-116840968	HepG2	liver:	n/a	n/a
11	POLR2A	chr9:116840008-116841137	HepG2	liver:	n/a	n/a
12	HEY1	chr9:116840328-116840821	HepG2	liver:	n/a	n/a
13	MBD4	chr9:116840249-116841223	HepG2	liver:	n/a	n/a
14	MAFF	chr9:116840445-116841240	HepG2	liver:	n/a	chr9:116840832-116840850
15	MBD4	chr9:116840232-116841048	HepG2	liver:	n/a	n/a
16	EP300	chr9:116840453-116841017	HepG2	liver:	n/a	chr9:116840621-116840631
17	MYBL2	chr9:116840152-116841184	HepG2	liver:	n/a	n/a
18	ARID3A	chr9:116840488-116840966	HepG2	liver:	n/a	n/a
19	SP1	chr9:116840307-116841154	HepG2	liver:	n/a	chr9:116840776-116840788 chr9:116840777-116840786 chr9:116840776-116840788 chr9:116840778-116840787
20	ELF1	chr9:116840425-116841058	HepG2	liver:	n/a	n/a
21	FOSL2	chr9:116840357-116841065	HepG2	liver:	n/a	n/a
22	CEBPB	chr9:116840439-116840891	HepG2	liver:	n/a	n/a
23	YY1	chr9:116840542-116840889	H1-hESC	embryonic stem cell:	n/a	n/a
24	TCF12	chr9:116840594-116841203	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr9:116835765-116840852	HepG2	liver:	n/a	n/a
26	FOSL2	chr9:116840394-116841063	HepG2	liver:	n/a	n/a
27	RAD21	chr9:116840370-116840995	HepG2	liver:	n/a	n/a
28	FOXA2	chr9:116840366-116840968	HepG2	liver:	n/a	n/a
29	RCOR1	chr9:116840396-116841338	HepG2	liver:	n/a	n/a
30	BACH1	chr9:116840658-116841126	K562	blood:	n/a	n/a
31	BACH1	chr9:116840541-116841228	H1-hESC	embryonic stem cell:	n/a	n/a
32	TCF12	chr9:116840213-116841302	A549	lung:	n/a	n/a
33	HNF4A	chr9:116840479-116840968	HepG2	liver:	n/a	n/a
34	TBP	chr9:116840397-116841025	HepG2	liver:	n/a	n/a
35	EP300	chr9:116840289-116841105	HepG2	liver:	n/a	chr9:116840621-116840631
36	FOXA1	chr9:116840272-116840975	HepG2	liver:	n/a	n/a
37	YY1	chr9:116840313-116841028	HepG2	liver:	n/a	n/a
38	NFIC	chr9:116839969-116841109	HepG2	liver:	n/a	chr9:116840185-116840202
39	REST	chr9:116840322-116841050	HepG2	liver:	n/a	chr9:116840648-116840668 chr9:116840659-116840668 chr9:116840648-116840668 chr9:116840652-116840665
40	RFX5	chr9:116840520-116840985	HepG2	liver:	n/a	n/a
41	MAFK	chr9:116840605-116841133	H1-hESC	embryonic stem cell:	n/a	chr9:116840834-116840849
42	ZBTB7A	chr9:116840435-116840917	HepG2	liver:	n/a	chr9:116840780-116840794
43	TAL1	chr9:116840721-116840991	K562	blood:	n/a	n/a
44	FOXA1	chr9:116840399-116841000	HepG2	liver:	n/a	n/a
45	HDAC2	chr9:116840357-116841065	HepG2	liver:	n/a	chr9:116840649-116840668
46	NFIC	chr9:116840081-116841423	ECC-1	luminal epithelium:	n/a	chr9:116840185-116840202
47	ZBTB7A	chr9:116840441-116840905	HepG2	liver:	n/a	chr9:116840780-116840794
48	JUND	chr9:116840463-116840843	HepG2	liver:	n/a	n/a
49	MYBL2	chr9:116840195-116841273	HepG2	liver:	n/a	n/a
50	POLR2A	chr9:116831402-116841083	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
AMBP	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10982058	1.00[ASN][1000 genomes]
rs10982061	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10982063	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13283242	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13302854	0.91[ASN][1000 genomes]
rs6478061	0.82[EUR][1000 genomes]
rs71503586	0.97[ASN][1000 genomes]
rs73560335	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
2	esv2422396	chr9:116792944-117354862	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
3	nsv466514	chr9:116810890-116867054	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv615222	chr9:116810890-116867054	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	esv2422492	chr9:116811294-117366643	Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	155 gene(s)	inside rSNPs	diseases
6	esv2761285	chr9:116811897-117103268	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	128 gene(s)	inside rSNPs	diseases
7	nsv466515	chr9:116814661-116867054	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv615223	chr9:116814661-116867054	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv528822	chr9:116815777-116867054	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv466516	chr9:116815777-116867054	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv466518	chr9:116815777-116867054	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv466519	chr9:116815777-116867054	Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv466520	chr9:116815777-116867054	Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv466521	chr9:116815777-116867054	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
15	nsv466522	chr9:116815777-116867054	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
16	nsv466523	chr9:116815777-116867054	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
17	nsv471319	chr9:116815777-116867054	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
18	nsv615224	chr9:116815777-116867054	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
19	nsv466524	chr9:116826842-116867054	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv466525	chr9:116826842-116867054	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv615225	chr9:116826842-116867054	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	esv996359	chr9:116839001-116847886	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116837200-116842400	Enhancers	A549	lung
2	chr9:116839000-116841600	Enhancers	Rectal Mucosa Donor 31	rectum
3	chr9:116839000-116845200	Enhancers	Stomach Mucosa	stomach
4	chr9:116839600-116841200	Enhancers	Gastric	stomach
5	chr9:116839800-116841000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:116839800-116841000	Enhancers	Esophagus	oesophagus
7	chr9:116839800-116841400	Enhancers	Colonic Mucosa	Colon
8	chr9:116839800-116841400	Enhancers	Duodenum Mucosa	Duodenum
9	chr9:116839800-116841800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:116839800-116846200	Enhancers	Fetal Intestine Small	intestine
11	chr9:116840000-116841000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr9:116840000-116841400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr9:116840000-116841600	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr9:116840000-116847000	Enhancers	Fetal Intestine Large	intestine
15	chr9:116840400-116841000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr9:116840400-116841000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:116840400-116841200	Enhancers	Lung	lung
18	chr9:116840600-116841200	Enhancers	K562	blood
19	chr9:116840600-116841400	Flanking Active TSS	Liver	Liver
20	chr9:116840800-116841000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:116840800-116841000	Bivalent Enhancer	Placenta	Placenta
22	chr9:116840800-116841400	Flanking Active TSS	HepG2	liver
23	chr9:116840800-116842800	Weak transcription	Fetal Lung	lung
24	chr9:116840800-116844600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:116840800-116845200	Enhancers	Pancreas	Pancrea

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