Variant report

Variant	rs2116403
Chromosome Location	chr9:116842799-116842800
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	MYBL2	chr9:116842304-116845289	HepG2	liver:	n/a	n/a
2	HEY1	chr9:116842588-116845189	HepG2	liver:	n/a	n/a
3	SP1	chr9:116842406-116845227	A549	lung:	n/a	chr9:116844352-116844366 chr9:116843251-116843260
4	FOXA2	chr9:116842738-116843938	HepG2	liver:	n/a	chr9:116843033-116843045
5	MAX	chr9:116842570-116844180	A549	lung:	n/a	chr9:116843452-116843462
6	TCF12	chr9:116842319-116845308	A549	lung:	n/a	chr9:116843446-116843456
7	POLR2A	chr9:116842289-116844808	HepG2	liver:	n/a	n/a
8	POLR2A	chr9:116842309-116843002	HepG2	liver:	n/a	n/a
9	REST	chr9:116842485-116845193	A549	lung:	n/a	n/a
10	EP300	chr9:116842281-116844185	A549	lung:	n/a	chr9:116843339-116843349
11	ELF1	chr9:116842783-116843523	A549	lung:	n/a	n/a
12	ATF3	chr9:116842433-116843590	A549	lung:	n/a	n/a
13	SP1	chr9:116842368-116845209	A549	lung:	n/a	chr9:116844352-116844366 chr9:116843251-116843260
14	FOXA2	chr9:116842795-116844061	A549	lung:	n/a	chr9:116843033-116843045
15	POLR2A	chr9:116842272-116845223	HepG2	liver:	n/a	n/a
16	CEBPB	chr9:116842549-116843727	A549	lung:	n/a	n/a
17	TBP	chr9:116842720-116845074	HepG2	liver:	n/a	n/a
18	MAX	chr9:116842190-116845354	HepG2	liver:	n/a	chr9:116843452-116843462 chr9:116844878-116844888
19	POLR2A	chr9:116842693-116845034	HepG2	liver:	n/a	n/a
20	EP300	chr9:116842579-116845190	HepG2	liver:	n/a	chr9:116843339-116843349
21	FOSL2	chr9:116842296-116844109	A549	lung:	n/a	n/a
22	MYBL2	chr9:116842527-116845298	HepG2	liver:	n/a	n/a
23	EP300	chr9:116842411-116844005	A549	lung:	n/a	chr9:116843339-116843349
24	MBD4	chr9:116842569-116845208	HepG2	liver:	n/a	n/a
25	SP1	chr9:116842688-116845098	HepG2	liver:	n/a	chr9:116844352-116844366 chr9:116843251-116843260
26	ARID3A	chr9:116842638-116844032	HepG2	liver:	n/a	n/a
27	GATA3	chr9:116842475-116843922	A549	lung:	n/a	chr9:116843272-116843282
28	NFIC	chr9:116842323-116845215	HepG2	liver:	n/a	n/a
29	BCL3	chr9:116842282-116843923	A549	lung:	n/a	chr9:116843045-116843054 chr9:116843046-116843055
30	RCOR1	chr9:116842382-116842814	HepG2	liver:	n/a	n/a
31	POLR2A	chr9:116842401-116845170	HepG2	liver:	n/a	n/a
32	MBD4	chr9:116842397-116843842	HepG2	liver:	n/a	n/a
33	POLR2A	chr9:116842329-116845543	HepG2	liver:	n/a	n/a
34	TEAD4	chr9:116842438-116845262	HepG2	liver:	n/a	n/a
35	SIX5	chr9:116842284-116843620	A549	lung:	n/a	n/a
36	USF1	chr9:116842790-116843521	A549	lung:	n/a	n/a
37	NFIC	chr9:116842438-116844070	HepG2	liver:	n/a	n/a
38	EP300	chr9:116842781-116844723	HepG2	liver:	n/a	chr9:116843339-116843349
39	GABPA	chr9:116842769-116843499	A549	lung:	n/a	n/a
40	REST	chr9:116842598-116843410	A549	lung:	n/a	n/a
41	YY1	chr9:116842703-116843544	A549	lung:	n/a	chr9:116843251-116843262 chr9:116843087-116843109 chr9:116843098-116843106
42	MAX	chr9:116842352-116845390	A549	lung:	n/a	chr9:116843452-116843462 chr9:116844878-116844888
43	ELF1	chr9:116842745-116843687	HepG2	liver:	n/a	n/a
44	HEY1	chr9:116842309-116845278	HepG2	liver:	n/a	n/a
45	FOXA2	chr9:116842768-116844064	A549	lung:	n/a	chr9:116843033-116843045

No.	Distal block	Cell Line	Cell type
1	chr9:116837232..116841114-chr9:116841892..116845820,4	MCF-7	breast:
2	chr9:116841868..116844591-chr9:116846288..116849534,3	MCF-7	breast:
3	chr9:116836243..116838411-chr9:116841082..116842914,2	MCF-7	breast:
4	chr9:116842742..116844725-chr9:116847223..116849817,2	K562	blood:

Variant related genes	Relation type
AMBP	TF binding region
ENSG00000106927	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10116075	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10119159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759681	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10982059	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1982048	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2093785	0.81[CEU][hapmap]
rs2251680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2285055	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2761691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478062	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs7040719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7853169	0.81[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 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
23	nsv870215	chr9:116842614-117070344	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	124 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116839000-116845200	Enhancers	Stomach Mucosa	stomach
2	chr9:116839800-116846200	Enhancers	Fetal Intestine Small	intestine
3	chr9:116840000-116847000	Enhancers	Fetal Intestine Large	intestine
4	chr9:116840800-116842800	Weak transcription	Fetal Lung	lung
5	chr9:116840800-116844600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:116840800-116845200	Enhancers	Pancreas	Pancrea
7	chr9:116841200-116843600	Weak transcription	Lung	lung
8	chr9:116841400-116843000	Weak transcription	Colonic Mucosa	Colon
9	chr9:116841600-116845200	Enhancers	Fetal Kidney	kidney
10	chr9:116842000-116842800	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr9:116842400-116843000	Flanking Active TSS	A549	lung
12	chr9:116842400-116843200	Flanking Active TSS	HepG2	liver
13	chr9:116842400-116844800	Enhancers	Gastric	stomach
14	chr9:116842400-116844800	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr9:116842400-116845200	Flanking Active TSS	Liver	Liver
16	chr9:116842400-116845200	Enhancers	Duodenum Mucosa	Duodenum
17	chr9:116842600-116843800	Weak transcription	Small Intestine	intestine
18	chr9:116842600-116844800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:116842600-116845000	Enhancers	Rectal Mucosa Donor 29	rectum

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