Variant report

Variant	rs73446761
Chromosome Location	chr9:72874289-72874290
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	ELF1	chr9:72873749-72874348	K562	blood:	n/a	chr9:72874189-72874201
2	POLR2A	chr9:72873589-72874439	GM12891	blood:	n/a	n/a
3	POLR2A	chr9:72873239-72874366	HCT-116	colon:	n/a	n/a
4	MXI1	chr9:72873235-72874496	HepG2	liver:	n/a	n/a
5	POLR2A	chr9:72873412-72874835	GM12878	blood:	n/a	n/a
6	E2F6	chr9:72873105-72874295	H1-hESC	embryonic stem cell:	n/a	chr9:72873896-72873911 chr9:72873792-72873804 chr9:72873909-72873919 chr9:72873843-72873853 chr9:72873841-72873850 chr9:72874227-72874237
7	PAX5	chr9:72873649-72874308	GM12892	blood:	n/a	chr9:72873868-72873877 chr9:72874248-72874257 chr9:72873675-72873684
8	POLR2A	chr9:72873155-72874555	Hela-S3	cervix:	n/a	n/a
9	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
10	BCL11A	chr9:72874143-72874430	GM12878	blood:	n/a	n/a
11	MAX	chr9:72873058-72874712	HCT-116	colon:	n/a	chr9:72874255-72874264
12	MAX	chr9:72873069-72874808	ECC-1	luminal epithelium:	n/a	chr9:72874255-72874264
13	MAZ	chr9:72873421-72874456	HepG2	liver:	n/a	chr9:72874255-72874264
14	TCF12	chr9:72873660-72874350	GM12878	blood:	n/a	chr9:72874224-72874234
15	MAX	chr9:72873096-72874600	ECC-1	luminal epithelium:	n/a	chr9:72874255-72874264
16	EGR1	chr9:72873868-72874493	MCF-7	breast:	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 chr9:72874255-72874265 chr9:72874255-72874265 chr9:72874254-72874268
17	POLR2A	chr9:72873537-72874312	HepG2	liver:	n/a	n/a
18	CHD2	chr9:72873367-72874354	K562	blood:	n/a	chr9:72873802-72873812
19	MYC	chr9:72873673-72874311	HepG2	liver:	n/a	chr9:72874255-72874264
20	GATA1	chr9:72873523-72874962	PBDE	blood:	n/a	chr9:72874615-72874622 chr9:72874615-72874622 chr9:72874615-72874622 chr9:72874561-72874570
21	POLR2A	chr9:72872858-72874429	U87	brain:	n/a	n/a
22	TFAP2C	chr9:72873172-72874542	Hela-S3	cervix:	n/a	n/a
23	TAF1	chr9:72873605-72874355	GM12891	blood:	n/a	n/a
24	E2F6	chr9:72873642-72874348	K562	blood:	n/a	chr9:72873896-72873911 chr9:72873792-72873804 chr9:72873909-72873919 chr9:72873843-72873853 chr9:72873841-72873850 chr9:72874227-72874237
25	MYC	chr9:72873032-72874620	NB4	blood:	n/a	chr9:72874255-72874264
26	ARID3A	chr9:72873550-72874300	HepG2	liver:	n/a	n/a
27	RELA	chr9:72873238-72874490	GM19099	blood:	n/a	n/a
28	NRF1	chr9:72873391-72874428	GM12878	blood:	n/a	chr9:72873840-72873851 chr9:72873839-72873850 chr9:72873840-72873849 chr9:72873840-72873854 chr9:72873837-72873851
29	YY1	chr9:72873636-72874342	GM12892	blood:	n/a	chr9:72873796-72873807 chr9:72873901-72873912
30	YY1	chr9:72873663-72874395	ECC-1	luminal epithelium:	n/a	chr9:72873796-72873807 chr9:72873901-72873912
31	E2F4	chr9:72873406-72874353	Hela-S3	cervix:	n/a	chr9:72873896-72873911 chr9:72873792-72873804 chr9:72873909-72873919 chr9:72873843-72873853 chr9:72873841-72873850 chr9:72874227-72874237 chr9:72873849-72873860
32	POLR2A	chr9:72873428-72874320	A549	lung:	n/a	n/a
33	YY1	chr9:72873666-72874388	HepG2	liver:	n/a	chr9:72873796-72873807 chr9:72873901-72873912
34	POLR2A	chr9:72873463-72874320	U87	brain:	n/a	n/a
35	MAX	chr9:72873114-72874532	A549	lung:	n/a	chr9:72874255-72874264
36	EBF1	chr9:72873555-72874762	GM12878	blood:	n/a	chr9:72874314-72874325 chr9:72874314-72874324 chr9:72874315-72874324
37	MAZ	chr9:72873179-72874585	K562	blood:	n/a	chr9:72874255-72874264
38	STAT3	chr9:72873919-72874832	MCF10A-Er-Src	breast:	n/a	chr9:72874739-72874747 chr9:72874740-72874752 chr9:72874509-72874532
39	HCFC1	chr9:72873512-72874525	K562	blood:	n/a	n/a
40	POLR2A	chr9:72873463-72874313	U87	brain:	n/a	n/a
41	BCLAF1	chr9:72873088-72874424	GM12878	blood:	n/a	chr9:72873786-72873795 chr9:72873899-72873912
42	CHD2	chr9:72873405-72874577	Hela-S3	cervix:	n/a	chr9:72873802-72873812
43	STAT3	chr9:72874222-72874558	MCF10A-Er-Src	breast:	n/a	chr9:72874509-72874532
44	KAT2A	chr9:72873846-72874297	Hela-S3	cervix:	n/a	n/a
45	UBTF	chr9:72873135-72874495	K562	blood:	n/a	n/a
46	POLR2A	chr9:72873323-72874700	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr9:72872909-72874290	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr9:72873118-72874334	HL-60	blood:	n/a	n/a
49	MYC	chr9:72874205-72874293	MCF-7	breast:	n/a	chr9:72874255-72874264
50	POLR2A	chr9:72872279-72874875	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:72874251-72874301	AoSMC	blood vessel:	n/a
2	chr9:72874251-72874301	GM12878	blood:	n/a
3	chr9:72874251-72874301	AG09319	gingival:	n/a
4	chr9:72874251-72874301	IMR90	lung:	fetal
5	chr9:72874251-72874301	LNCaP	prostate:	n/a
6	chr9:72874251-72874301	AG04449	skin:	fetal
7	chr9:72874251-72874301	ProgFib	skin:	n/a
8	chr9:72874251-72874301	HNPCEpiC	eye:	n/a
9	chr9:72874251-72874301	HL-60	blood:	n/a
10	chr9:72874251-72874301	A549	lung:	n/a
11	chr9:72874251-72874301	BE2_C	brain:	n/a
12	chr9:72874251-72874301	SAEC	small airway:	n/a
13	chr9:72874251-72874301	HEK293	kidney:	embryo
14	chr9:72874251-72874301	NH-A	brain:	n/a
15	chr9:72874251-72874301	HPAEpiC	pulmonary alveolar:	n/a
16	chr9:72874251-72874301	MCF-7	breast:	n/a
17	chr9:72874251-72874301	HCF	heart:	n/a
18	chr9:72874251-72874301	Hepatocyte	liver:	n/a
19	chr9:72874251-72874301	CMK	blood:	n/a
20	chr9:72874251-72874301	ovcar-3	ovarian:	n/a
21	chr9:72874251-72874301	HRE	kidney:	n/a
22	chr9:72874251-72874301	HAEpiC	amniotic membrane:	n/a
23	chr9:72874251-72874301	ECC-1	luminal epithelium:	n/a
24	chr9:72874251-72874301	RPTEC	kidney:	n/a
25	chr9:72874251-72874301	Hela-S3	cervix:	n/a
26	chr9:72874251-72874301	SK-N-MC	brain:	n/a
27	chr9:72874251-72874301	Caco-2	colon:	n/a
28	chr9:72874251-72874301	SKMC	muscle:	n/a
29	chr9:72874251-72874301	GM19239	blood:	n/a
30	chr9:72874251-72874301	HMEC	breast:	n/a
31	chr9:72874251-72874301	BJ	skin:	n/a
32	chr9:72874251-72874301	GM06990	blood:	n/a
33	chr9:72874251-72874301	PrEC	prostate:	n/a
34	chr9:72874251-72874301	HCT-116	colon:	n/a
35	chr9:72874251-72874301	GM12892	blood:	n/a
36	chr9:72874251-72874301	K562	blood:	n/a
37	chr9:72874251-72874301	HCM	heart:	n/a
38	chr9:72874251-72874301	SK-N-SH	brain:	n/a
39	chr9:72874251-72874301	GM12891	blood:	n/a
40	chr9:72874251-72874301	NHDF-neo	bronchial:	n/a
41	chr9:72874251-72874301	HRCEpiC	kidney:	n/a
42	chr9:72874251-72874301	AG09309	skin:	n/a
43	chr9:72874251-72874301	AG10803	skin:	n/a
44	chr9:72874251-72874301	AG04450	lung:	fetal
45	chr9:72874251-72874301	HEEpiC	esophagus:	n/a
46	chr9:72874251-72874301	HUVEC	blood vessel:	n/a
47	chr9:72874251-72874301	NHBE	bronchial:	n/a
48	chr9:72874251-72874301	H1-hESC	embryonic stem cell:	embryo
49	chr9:72874251-72874301	PFSK-1	brain:	n/a
50	chr9:72874251-72874301	T-47D	breast:	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	chr19:50083124..50083902-chr9:72873392..72874324,2	Hela-S3	cervix:
4	chr3:57678149..57678816-chr9:72873480..72874476,2	Hela-S3	cervix:
5	chr16:87426140..87426868-chr9:72873483..72874472,2	Hela-S3	cervix:
6	chr15:70388787..70390778-chr9:72873616..72875278,2	MCF-7	breast:
7	chr1:145469925..145470568-chr9:72873795..72874322,2	Hela-S3	cervix:
8	chr1:11968045..11968807-chr9:72873530..72874374,2	HCT-116	colon:
9	chr9:72873909..72874649-chrX:48432799..48433571,2	Hela-S3	cervix:
10	chr9:72373387..72376208-chr9:72873924..72875696,2	K562	blood:
11	chr9:4298313..4298905-chr9:72873435..72874413,2	Hela-S3	cervix:

Variant related genes	Relation type
SMC5-AS1	TF binding region
SMC5-AS1	CpG island
ENSG00000140525	Chromatin interaction
ENSG00000181039	Chromatin interaction
ENSG00000119138	Chromatin interaction
ENSG00000121851	Chromatin interaction
ENSG00000107249	Chromatin interaction
ENSG00000188647	Chromatin interaction
ENSG00000140941	Chromatin interaction
ENSG00000174839	Chromatin interaction
ENSG00000102317	Chromatin interaction
ENSG00000140332	Chromatin interaction
ENSG00000204620	Chromatin interaction
ENSG00000142546	Chromatin interaction
ENSG00000199347	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11142463	1.00[AMR][1000 genomes]
rs12341550	1.00[AMR][1000 genomes]
rs58121128	1.00[AMR][1000 genomes]
rs58305401	1.00[AMR][1000 genomes]
rs73446770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73446796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73448656	1.00[AMR][1000 genomes]
rs73448659	1.00[AMR][1000 genomes]
rs73448667	1.00[AMR][1000 genomes]
rs73448674	1.00[AMR][1000 genomes]
rs73448682	1.00[AMR][1000 genomes]
rs73448908	1.00[AMR][1000 genomes]
rs73451417	1.00[AMR][1000 genomes]
rs73451448	1.00[AMR][1000 genomes]
rs73451458	1.00[AMR][1000 genomes]
rs73452704	1.00[AMR][1000 genomes]
rs73452711	1.00[AMR][1000 genomes]
rs73452717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73452734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73454775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73456672	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73458721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73458732	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73460504	1.00[AMR][1000 genomes]
rs73460506	1.00[AMR][1000 genomes]
rs73460510	1.00[AMR][1000 genomes]
rs73460516	1.00[AMR][1000 genomes]
rs73460525	1.00[AMR][1000 genomes]
rs73650513	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	chr9:72872800-72874400	Active TSS	Brain Anterior Caudate	brain
12	chr9:72872800-72874400	Active TSS	Stomach Mucosa	stomach
13	chr9:72872800-72875000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:72872800-72875000	Active TSS	Fetal Intestine Large	intestine
15	chr9:72872800-72875000	Active TSS	Psoas Muscle	Psoas
16	chr9:72872800-72875200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:72872800-72875400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr9:72872800-72876200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr9:72873000-72874400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr9:72873000-72874400	Active TSS	Fetal Brain Female	brain
21	chr9:72873000-72874400	Active TSS	Thymus	Thymus
22	chr9:72873000-72874600	Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr9:72873000-72874600	Active TSS	Brain Hippocampus Middle	brain
24	chr9:72873000-72874600	Active TSS	Brain Substantia Nigra	brain
25	chr9:72873000-72874800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:72873000-72874800	Active TSS	Esophagus	oesophagus
27	chr9:72873000-72875000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:72873000-72875000	Active TSS	Duodenum Mucosa	Duodenum
29	chr9:72873000-72875000	Active TSS	Left Ventricle	heart
30	chr9:72873000-72875000	Active TSS	Right Ventricle	heart
31	chr9:72873000-72875400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:72873000-72875400	Active TSS	Fetal Kidney	kidney
33	chr9:72873000-72875400	Active TSS	A549	lung
34	chr9:72873000-72876000	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr9:72873200-72874400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
36	chr9:72873200-72874400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr9:72873200-72874400	Active TSS	Liver	Liver
38	chr9:72873200-72874600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr9:72873200-72874800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:72873200-72874800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr9:72873200-72874800	Active TSS	Lung	lung
42	chr9:72873200-72874800	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr9:72873200-72874800	Active TSS	Small Intestine	intestine
44	chr9:72873200-72874800	Bivalent/Poised TSS	HepG2	liver
45	chr9:72873200-72875000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr9:72873200-72875000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:72873200-72875000	Active TSS	Gastric	stomach
48	chr9:72873200-72875000	Active TSS	Ovary	ovary
49	chr9:72873200-72875200	Active TSS	H9 Cell Line	embryonic stem cell
50	chr9:72873200-72875200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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