Variant report

Variant	rs7046628
Chromosome Location	chr9:97682824-97682825
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	NFIC	chr9:97682596-97683925	SK-N-SH	brain:	n/a	n/a
2	MAX	chr9:97681372-97685528	A549	lung:	n/a	n/a
3	RCOR1	chr9:97682648-97686148	IMR90	lung:	n/a	n/a
4	SP1	chr9:97681342-97685519	A549	lung:	n/a	n/a
5	TAF1	chr9:97682599-97683214	SK-N-SH	brain:	n/a	n/a
6	REST	chr9:97682505-97685348	A549	lung:	n/a	chr9:97684506-97684526 chr9:97682757-97682770 chr9:97682800-97682813 chr9:97682940-97682950 chr9:97684641-97684654
7	POLR2A	chr9:97682706-97684912	ProgFib	skin:	n/a	n/a
8	EP300	chr9:97682702-97683151	SK-N-SH_RA	brain:	n/a	chr9:97682882-97682896
9	EP300	chr9:97681350-97683738	A549	lung:	n/a	chr9:97683352-97683366 chr9:97683353-97683367 chr9:97683357-97683371 chr9:97682882-97682896
10	FOSL2	chr9:97681546-97685898	A549	lung:	n/a	n/a
11	YY1	chr9:97682638-97682956	A549	lung:	n/a	n/a
12	EGR1	chr9:97681824-97682891	HCT-116	colon:	n/a	n/a
13	CTCF	chr9:97682700-97682850	AG09319	gingival:	n/a	chr9:97682753-97682761
14	REST	chr9:97682636-97683064	SK-N-SH	brain:	n/a	chr9:97682757-97682770 chr9:97682800-97682813 chr9:97682940-97682950
15	POLR2A	chr9:97682660-97682862	A549	lung:	n/a	n/a
16	RAD21	chr9:97682587-97683277	SK-N-SH_RA	brain:	n/a	n/a
17	SP1	chr9:97681324-97685508	A549	lung:	n/a	n/a
18	BCL3	chr9:97681559-97685224	A549	lung:	n/a	n/a
19	POLR2A	chr9:97682617-97682853	A549	lung:	n/a	n/a
20	JUND	chr9:97682622-97683128	A549	lung:	n/a	n/a
21	GATA3	chr9:97681311-97685467	A549	lung:	n/a	n/a
22	TAF1	chr9:97682484-97683748	A549	lung:	n/a	n/a
23	GATA3	chr9:97682576-97683912	SK-N-SH	brain:	n/a	n/a
24	CEBPB	chr9:97682787-97683173	IMR90	lung:	n/a	n/a
25	EP300	chr9:97682661-97683162	SK-N-SH_RA	brain:	n/a	chr9:97682882-97682896
26	EP300	chr9:97682605-97684015	SK-N-SH	brain:	n/a	chr9:97683352-97683366 chr9:97683353-97683367 chr9:97683357-97683371 chr9:97682882-97682896
27	TCF12	chr9:97681294-97685653	A549	lung:	n/a	chr9:97685588-97685595
28	CEBPB	chr9:97682745-97683201	A549	lung:	n/a	n/a
29	POLR2A	chr9:97682580-97683221	A549	lung:	n/a	n/a
30	RAD21	chr9:97682658-97683072	SK-N-SH_RA	brain:	n/a	n/a
31	SIN3AK20	chr9:97682676-97683733	A549	lung:	n/a	n/a
32	SIX5	chr9:97681767-97685733	A549	lung:	n/a	n/a
33	TEAD4	chr9:97682550-97683768	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr9:97682640-97682980	A549	lung:	n/a	n/a
35	CTCF	chr9:97682740-97682890	AG04449	skin:	n/a	chr9:97682753-97682761
36	BCL3	chr9:97681414-97683736	A549	lung:	n/a	n/a
37	EP300	chr9:97682704-97683865	SK-N-SH	brain:	n/a	chr9:97683352-97683366 chr9:97683353-97683367 chr9:97683357-97683371 chr9:97682882-97682896
38	JUND	chr9:97681585-97682969	MCF-7	breast:	n/a	n/a
39	MAX	chr9:97682526-97683748	A549	lung:	n/a	n/a
40	GATA3	chr9:97682589-97683840	SK-N-SH	brain:	n/a	n/a
41	TCF12	chr9:97682503-97683929	SK-N-SH	brain:	n/a	n/a
42	SIN3AK20	chr9:97682724-97683265	A549	lung:	n/a	n/a
43	JUND	chr9:97682583-97683799	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr9:97682531-97684225	SK-N-SH	brain:	n/a	n/a
45	E2F6	chr9:97682527-97683398	A549	lung:	n/a	chr9:97683289-97683298
46	TCF12	chr9:97682502-97683888	SK-N-SH	brain:	n/a	n/a
47	TEAD4	chr9:97682533-97683881	SK-N-SH	brain:	n/a	n/a
48	PBX3	chr9:97682646-97683881	SK-N-SH	brain:	n/a	n/a
49	FOXA2	chr9:97681553-97682988	A549	lung:	n/a	n/a
50	CTCF	chr9:97682700-97682850	NHDF-neo	bronchial:	n/a	chr9:97682753-97682761

No.	Distal block	Cell Line	Cell type
1	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
2	chr9:97679968..97683217-chr9:97810510..97812408,3	MCF-7	breast:
3	chr9:97572097..97590438-chr9:97672990..97690806,63	MCF-7	breast:
4	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
5	chr9:97678927..97686235-chr9:97889117..97896057,11	MCF-7	breast:
6	chr9:97558473..97564935-chr9:97678907..97687123,11	MCF-7	breast:
7	chr9:97562492..97588737-chr9:97670126..97691056,102	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000230815	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000252153	Chromatin interaction
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1004813	1.00[AMR][1000 genomes]
rs10512251	1.00[AMR][1000 genomes]
rs12684072	1.00[AMR][1000 genomes]
rs12684777	1.00[AMR][1000 genomes]
rs12685442	1.00[AMR][1000 genomes]
rs1543848	1.00[AMR][1000 genomes]
rs16911870	1.00[AMR][1000 genomes]
rs16911899	1.00[AMR][1000 genomes]
rs28374530	1.00[AMR][1000 genomes]
rs55795857	1.00[AMR][1000 genomes]
rs55932459	1.00[AMR][1000 genomes]
rs7024881	1.00[AMR][1000 genomes]
rs7043275	1.00[AMR][1000 genomes]
rs72750306	1.00[AMR][1000 genomes]
rs72750343	1.00[AMR][1000 genomes]
rs72750345	1.00[AMR][1000 genomes]
rs72750349	1.00[AMR][1000 genomes]
rs72750353	1.00[AMR][1000 genomes]
rs72750354	1.00[AMR][1000 genomes]
rs72750355	1.00[AMR][1000 genomes]
rs72750360	1.00[AMR][1000 genomes]
rs72750361	1.00[AMR][1000 genomes]
rs72750363	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
2	chr9:97661600-97686200	Weak transcription	Primary T cells from cord blood	blood
3	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr9:97671000-97684200	Weak transcription	Small Intestine	intestine
5	chr9:97675000-97684400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:97675400-97684000	Weak transcription	Psoas Muscle	Psoas
7	chr9:97676600-97683000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:97676600-97684200	Weak transcription	Colonic Mucosa	Colon
9	chr9:97676800-97683400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:97677000-97684000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr9:97677400-97688600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:97678000-97683000	Weak transcription	Fetal Intestine Large	intestine
13	chr9:97678000-97684400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:97679000-97686400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr9:97679200-97683200	Enhancers	Stomach Mucosa	stomach
16	chr9:97679200-97687200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:97679400-97687000	Enhancers	Fetal Heart	heart
18	chr9:97679800-97684000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:97679800-97684000	Weak transcription	Fetal Intestine Small	intestine
20	chr9:97679800-97684200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:97679800-97684400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr9:97679800-97684400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:97679800-97686200	Weak transcription	Fetal Thymus	thymus
24	chr9:97680000-97683000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:97680000-97684200	Weak transcription	Fetal Brain Male	brain
26	chr9:97680000-97687600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:97680200-97688000	Weak transcription	Gastric	stomach
28	chr9:97680400-97685800	Enhancers	Right Ventricle	heart
29	chr9:97680400-97698000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:97680600-97683200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:97680600-97685000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:97680600-97686400	Enhancers	Ovary	ovary
33	chr9:97680600-97700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:97680800-97683000	Weak transcription	Brain Substantia Nigra	brain
35	chr9:97680800-97684600	Weak transcription	GM12878-XiMat	blood
36	chr9:97680800-97685000	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr9:97681000-97684200	Weak transcription	Pancreas	Pancrea
38	chr9:97681400-97684000	Enhancers	Hela-S3	cervix
39	chr9:97681400-97686200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:97681400-97686600	Enhancers	Right Atrium	heart
41	chr9:97681600-97683000	Enhancers	NH-A	brain
42	chr9:97681600-97683000	Enhancers	NHLF	lung
43	chr9:97681600-97683400	Enhancers	Esophagus	oesophagus
44	chr9:97681600-97683400	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr9:97681600-97683400	Enhancers	Osteobl	bone
46	chr9:97681600-97684600	Enhancers	Lung	lung
47	chr9:97681600-97684800	Enhancers	Fetal Muscle Trunk	muscle
48	chr9:97681600-97685800	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr9:97681600-97686000	Enhancers	Left Ventricle	heart
50	chr9:97681600-97686600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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