Variant report

Variant	rs73446762
Chromosome Location	chr9:72874604-72874605
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	POLR2A	chr9:72873412-72874835	GM12878	blood:	n/a	n/a
2	E2F4	chr9:72873336-72874672	MCF10A-Er-Src	breast:	n/a	chr9:72873896-72873911 chr9:72873792-72873804 chr9:72873909-72873919 chr9:72873843-72873853 chr9:72873841-72873850 chr9:72874227-72874237 chr9:72873849-72873860
3	MAX	chr9:72873058-72874712	HCT-116	colon:	n/a	chr9:72874255-72874264
4	MAX	chr9:72873069-72874808	ECC-1	luminal epithelium:	n/a	chr9:72874255-72874264
5	GATA1	chr9:72873523-72874962	PBDE	blood:	n/a	chr9:72874615-72874622 chr9:72874615-72874622 chr9:72874615-72874622 chr9:72874561-72874570
6	MYC	chr9:72873032-72874620	NB4	blood:	n/a	chr9:72874255-72874264
7	EBF1	chr9:72873555-72874762	GM12878	blood:	n/a	chr9:72874314-72874325 chr9:72874314-72874324 chr9:72874315-72874324
8	STAT3	chr9:72873919-72874832	MCF10A-Er-Src	breast:	n/a	chr9:72874739-72874747 chr9:72874740-72874752 chr9:72874509-72874532
9	POLR2A	chr9:72873323-72874700	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr9:72872279-72874875	HepG2	liver:	n/a	n/a
11	MAX	chr9:72872944-72874679	HepG2	liver:	n/a	chr9:72874255-72874264
12	POLR2A	chr9:72873203-72875053	GM12878	blood:	n/a	n/a
13	POLR2A	chr9:72872969-72874616	GM18505	blood:	n/a	n/a
14	EGR1	chr9:72873925-72874629	ECC-1	luminal epithelium:	n/a	chr9:72874254-72874265 chr9:72874247-72874260 chr9:72874256-72874265 chr9:72874253-72874266 chr9:72874253-72874267 chr9:72874252-72874267 chr9:72874253-72874266 chr9:72874254-72874265 chr9:72874253-72874266 chr9:72874191-72874201 chr9:72874255-72874265 chr9:72874255-72874265 chr9:72874254-72874268
15	EGR1	chr9:72873058-72874857	HCT-116	colon:	n/a	chr9:72874254-72874265 chr9:72874247-72874260 chr9:72874256-72874265 chr9:72874253-72874266 chr9:72874253-72874267 chr9:72874252-72874267 chr9:72873899-72873913 chr9:72874253-72874266 chr9:72874254-72874265 chr9:72874253-72874266 chr9:72874191-72874201 chr9:72873841-72873850 chr9:72874255-72874265 chr9:72874255-72874265 chr9:72874254-72874268
16	MXI1	chr9:72873413-72874652	Hela-S3	cervix:	n/a	n/a
17	E2F4	chr9:72873418-72874607	K562	blood:	n/a	chr9:72873896-72873911 chr9:72873792-72873804 chr9:72873909-72873919 chr9:72873843-72873853 chr9:72873841-72873850 chr9:72874227-72874237 chr9:72873849-72873860
18	POLR2A	chr9:72870291-72877116	IMR90	lung:	n/a	n/a
19	POLR2A	chr9:72873148-72874641	Raji	blood:	n/a	n/a
20	BACH1	chr9:72873430-72874662	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr9:72872881-72874728	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr9:72873421-72874654	H1-neurons	neurons:	n/a	n/a
23	CREB1	chr9:72873546-72874630	GM12878	blood:	n/a	n/a
24	MYC	chr9:72873162-72874701	MCF10A-Er-Src	breast:	n/a	chr9:72874255-72874264
25	MXI1	chr9:72873814-72874805	K562	blood:	n/a	n/a
26	POU2F2	chr9:72873618-72874610	GM12878	blood:	n/a	chr9:72873796-72873808
27	EGR1	chr9:72873258-72874740	HCT-116	colon:	n/a	chr9:72874254-72874265 chr9:72874247-72874260 chr9:72874256-72874265 chr9:72874253-72874266 chr9:72874253-72874267 chr9:72874252-72874267 chr9:72873899-72873913 chr9:72874253-72874266 chr9:72874254-72874265 chr9:72874253-72874266 chr9:72874191-72874201 chr9:72873841-72873850 chr9:72874255-72874265 chr9:72874255-72874265 chr9:72874254-72874268
28	POLR2A	chr9:72873394-72874654	H1-neurons	neurons:	n/a	n/a
29	RCOR1	chr9:72873521-72874610	HepG2	liver:	n/a	n/a
30	MAX	chr9:72873085-72874695	HepG2	liver:	n/a	chr9:72874255-72874264
31	ZNF263	chr9:72873100-72874662	HEK293-T-REx	kidney:	n/a	n/a
32	RELA	chr9:72873059-72874705	GM15510	blood:	n/a	n/a
33	NRF1	chr9:72873424-72874721	SK-N-SH	brain:	n/a	chr9:72873840-72873851 chr9:72873839-72873850 chr9:72873840-72873849 chr9:72873840-72873854 chr9:72873837-72873851
34	WRNIP1	chr9:72873185-72874777	GM12878	blood:	n/a	n/a
35	POLR2A	chr9:72873077-72874605	GM12878	blood:	n/a	n/a
36	MAX	chr9:72873139-72874649	MCF-7	breast:	n/a	chr9:72874255-72874264
37	MTA3	chr9:72873016-72874670	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:72873076-72874803	K562	blood:	n/a	n/a
39	MAX	chr9:72873284-72874619	Hela-S3	cervix:	n/a	chr9:72874255-72874264
40	RCOR1	chr9:72873140-72874670	K562	blood:	n/a	n/a
41	TCF12	chr9:72873088-72874828	A549	lung:	n/a	chr9:72874224-72874234
42	GABPA	chr9:72872961-72874635	MCF-7	breast:	n/a	chr9:72873840-72873851 chr9:72873840-72873849 chr9:72873840-72873854 chr9:72873837-72873851
43	POLR2A	chr9:72873239-72874780	Hela-S3	cervix:	n/a	n/a
44	MXI1	chr9:72873147-72874836	GM12878	blood:	n/a	n/a
45	STAT3	chr9:72874233-72874835	MCF10A-Er-Src	breast:	n/a	chr9:72874739-72874747 chr9:72874740-72874752 chr9:72874509-72874532
46	REST	chr9:72872838-72874765	H1-neurons	neurons:	n/a	chr9:72873133-72873146
47	HCFC1	chr9:72873119-72874823	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr9:72872724-72874788	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr9:72872975-72874674	HUVEC	blood vessel:	n/a	n/a
50	TBP	chr9:72873331-72874614	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:89787008..89787862-chr9:72873789..72874612,2	Hela-S3	cervix:
2	chr9:72872890..72875231-chr9:73027091..73030195,4	K562	blood:
3	chr15:70388787..70390778-chr9:72873616..72875278,2	MCF-7	breast:
4	chr9:72873909..72874649-chrX:48432799..48433571,2	Hela-S3	cervix:
5	chr9:72373387..72376208-chr9:72873924..72875696,2	K562	blood:

Variant related genes	Relation type
SMC5-AS1	TF binding region
ENSG00000140332	Chromatin interaction
ENSG00000204620	Chromatin interaction
ENSG00000102317	Chromatin interaction
ENSG00000188647	Chromatin interaction
ENSG00000119138	Chromatin interaction
ENSG00000140525	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs35534839	1.00[AMR][1000 genomes]
rs58615277	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59725916	1.00[AMR][1000 genomes]
rs60551452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446764	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446778	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446789	1.00[AFR][1000 genomes]
rs73446793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73448646	1.00[AMR][1000 genomes]
rs73448651	1.00[AMR][1000 genomes]
rs73448660	1.00[AMR][1000 genomes]
rs73448663	1.00[AMR][1000 genomes]
rs73448670	1.00[AMR][1000 genomes]
rs73448904	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73449496	1.00[AMR][1000 genomes]
rs73451455	1.00[AMR][1000 genomes]
rs73452732	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73452740	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73452742	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73452745	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73452756	1.00[AMR][1000 genomes]
rs73454766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73454769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73456610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73456638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv831615	chr9:72852705-73019692	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72870400-72874800	Active TSS	Right Atrium	heart
2	chr9:72870600-72875000	Active TSS	Aorta	Aorta
3	chr9:72870800-72875200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr9:72871000-72876200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr9:72871800-72875200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:72872000-72875000	Active TSS	Pancreas	Pancrea
7	chr9:72872200-72874800	Active TSS	Fetal Muscle Trunk	muscle
8	chr9:72872600-72875000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr9:72872600-72875000	Active TSS	HSMMtube	muscle
10	chr9:72872600-72875600	Active TSS	Brain Cingulate Gyrus	brain
11	chr9:72872800-72875000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:72872800-72875000	Active TSS	Fetal Intestine Large	intestine
13	chr9:72872800-72875000	Active TSS	Psoas Muscle	Psoas
14	chr9:72872800-72875200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr9:72872800-72875400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr9:72872800-72876200	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr9:72873000-72874800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:72873000-72874800	Active TSS	Esophagus	oesophagus
19	chr9:72873000-72875000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr9:72873000-72875000	Active TSS	Duodenum Mucosa	Duodenum
21	chr9:72873000-72875000	Active TSS	Left Ventricle	heart
22	chr9:72873000-72875000	Active TSS	Right Ventricle	heart
23	chr9:72873000-72875400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:72873000-72875400	Active TSS	Fetal Kidney	kidney
25	chr9:72873000-72875400	Active TSS	A549	lung
26	chr9:72873000-72876000	Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr9:72873200-72874800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:72873200-72874800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:72873200-72874800	Active TSS	Lung	lung
30	chr9:72873200-72874800	Active TSS	Sigmoid Colon	Sigmoid Colon
31	chr9:72873200-72874800	Active TSS	Small Intestine	intestine
32	chr9:72873200-72874800	Bivalent/Poised TSS	HepG2	liver
33	chr9:72873200-72875000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr9:72873200-72875000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:72873200-72875000	Active TSS	Gastric	stomach
36	chr9:72873200-72875000	Active TSS	Ovary	ovary
37	chr9:72873200-72875200	Active TSS	H9 Cell Line	embryonic stem cell
38	chr9:72873200-72875200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr9:72873200-72875200	Active TSS	Brain Angular Gyrus	brain
40	chr9:72873400-72874800	Active TSS	Placenta	Placenta
41	chr9:72873400-72874800	Active TSS	Fetal Stomach	stomach
42	chr9:72873400-72875000	Active TSS	Fetal Lung	lung
43	chr9:72873400-72875000	Active TSS	Placenta Amnion	Placenta Amnion
44	chr9:72873400-72875200	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr9:72873400-72875200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:72873400-72875400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr9:72873400-72875400	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr9:72873400-72875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr9:72873400-72875400	Active TSS	NHDF-Ad	bronchial
50	chr9:72873400-72876000	Active TSS	iPS-15b Cell Line	embryonic stem cell

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