Variant report

Variant	rs943533
Chromosome Location	chr9:72873766-72873767
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	chr9:72873200-72874273	GM12892	blood:	n/a	n/a
2	ELF1	chr9:72873749-72874348	K562	blood:	n/a	chr9:72874189-72874201
3	POLR2A	chr9:72873589-72874439	GM12891	blood:	n/a	n/a
4	POLR2A	chr9:72873239-72874366	HCT-116	colon:	n/a	n/a
5	TAF1	chr9:72873710-72874027	PFSK-1	brain:	n/a	n/a
6	MXI1	chr9:72873235-72874496	HepG2	liver:	n/a	n/a
7	POLR2A	chr9:72873412-72874835	GM12878	blood:	n/a	n/a
8	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
9	MAX	chr9:72873640-72874008	K562	blood:	n/a	n/a
10	FOXA2	chr9:72873622-72874057	A549	lung:	n/a	n/a
11	PAX5	chr9:72873649-72874308	GM12892	blood:	n/a	chr9:72873868-72873877 chr9:72874248-72874257 chr9:72873675-72873684
12	POLR2A	chr9:72873155-72874555	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr9:72873557-72874210	SK-N-SH	brain:	n/a	n/a
14	JUN	chr9:72873626-72874083	K562	blood:	n/a	chr9:72873676-72873685 chr9:72873805-72873814
15	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
16	MAX	chr9:72873058-72874712	HCT-116	colon:	n/a	chr9:72874255-72874264
17	MAX	chr9:72873069-72874808	ECC-1	luminal epithelium:	n/a	chr9:72874255-72874264
18	MAZ	chr9:72873421-72874456	HepG2	liver:	n/a	chr9:72874255-72874264
19	POLR2A	chr9:72873437-72874180	PANC-1	pancreas:	n/a	n/a
20	YY1	chr9:72873596-72874222	SK-N-SH_RA	brain:	n/a	chr9:72873796-72873807 chr9:72873901-72873912
21	TCF12	chr9:72873660-72874350	GM12878	blood:	n/a	chr9:72874224-72874234
22	E2F6	chr9:72873315-72874130	A549	lung:	n/a	chr9:72873896-72873911 chr9:72873792-72873804 chr9:72873909-72873919 chr9:72873843-72873853 chr9:72873841-72873850
23	POLR2A	chr9:72873562-72874209	HUVEC	blood vessel:	n/a	n/a
24	MAX	chr9:72873096-72874600	ECC-1	luminal epithelium:	n/a	chr9:72874255-72874264
25	YY1	chr9:72873370-72874169	ECC-1	luminal epithelium:	n/a	chr9:72873796-72873807 chr9:72873901-72873912
26	MBD4	chr9:72873365-72873893	HepG2	liver:	n/a	n/a
27	E2F4	chr9:72873758-72874191	GM12878	blood:	n/a	chr9:72873896-72873911 chr9:72873792-72873804 chr9:72873909-72873919 chr9:72873843-72873853 chr9:72873841-72873850 chr9:72873849-72873860
28	POLR2A	chr9:72873537-72874312	HepG2	liver:	n/a	n/a
29	CHD2	chr9:72873367-72874354	K562	blood:	n/a	chr9:72873802-72873812
30	MYC	chr9:72873673-72874311	HepG2	liver:	n/a	chr9:72874255-72874264
31	GATA1	chr9:72873523-72874962	PBDE	blood:	n/a	chr9:72874615-72874622 chr9:72874615-72874622 chr9:72874615-72874622 chr9:72874561-72874570
32	POLR2A	chr9:72872858-72874429	U87	brain:	n/a	n/a
33	MYBL2	chr9:72873327-72874066	HepG2	liver:	n/a	n/a
34	TFAP2C	chr9:72873172-72874542	Hela-S3	cervix:	n/a	n/a
35	ZBTB33	chr9:72873671-72874156	GM12878	blood:	n/a	chr9:72873853-72873868 chr9:72873892-72873907 chr9:72873898-72873908
36	POLR2A	chr9:72873448-72874286	K562	blood:	n/a	n/a
37	GABPA	chr9:72873745-72874205	K562	blood:	n/a	chr9:72873840-72873851 chr9:72873840-72873849 chr9:72873840-72873854 chr9:72873837-72873851
38	MYC	chr9:72873712-72874097	H1-hESC	embryonic stem cell:	n/a	n/a
39	TAF1	chr9:72873605-72874355	GM12891	blood:	n/a	n/a
40	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
41	MYC	chr9:72873032-72874620	NB4	blood:	n/a	chr9:72874255-72874264
42	ZBTB33	chr9:72873658-72874162	HepG2	liver:	n/a	chr9:72873853-72873868 chr9:72873892-72873907 chr9:72873898-72873908
43	POLR2A	chr9:72872979-72874209	HepG2	liver:	n/a	n/a
44	STAT5A	chr9:72873593-72874066	GM12878	blood:	n/a	chr9:72873798-72873810
45	POU2F2	chr9:72873401-72874176	GM12891	blood:	n/a	chr9:72873796-72873808
46	ARID3A	chr9:72873550-72874300	HepG2	liver:	n/a	n/a
47	RELA	chr9:72873238-72874490	GM19099	blood:	n/a	n/a
48	NRF1	chr9:72873391-72874428	GM12878	blood:	n/a	chr9:72873840-72873851 chr9:72873839-72873850 chr9:72873840-72873849 chr9:72873840-72873854 chr9:72873837-72873851
49	YY1	chr9:72873636-72874342	GM12892	blood:	n/a	chr9:72873796-72873807 chr9:72873901-72873912
50	YY1	chr9:72873663-72874395	ECC-1	luminal epithelium:	n/a	chr9:72873796-72873807 chr9:72873901-72873912

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:72873728-72873778	GM19239	blood:	n/a
2	chr9:72873728-72873778	HEK293	kidney:	embryo
3	chr9:72873728-72873778	NH-A	brain:	n/a
4	chr9:72873728-72873778	MCF10A-Er-Src	breast:	n/a
5	chr9:72873728-72873778	HAEpiC	amniotic membrane:	n/a
6	chr9:72873728-72873778	HL-60	blood:	n/a
7	chr9:72873728-72873778	GM06990	blood:	n/a
8	chr9:72873728-72873778	BE2_C	brain:	n/a
9	chr9:72873728-72873778	HMEC	breast:	n/a
10	chr9:72873728-72873778	Hela-S3	cervix:	n/a
11	chr9:72873728-72873778	HIPEpiC	eye:	n/a
12	chr9:72873728-72873778	HCT-116	colon:	n/a
13	chr9:72873728-72873778	U87	brain:	n/a
14	chr9:72873728-72873778	AoSMC	blood vessel:	n/a
15	chr9:72873728-72873778	SK-N-SH_RA	brain:	n/a
16	chr9:72873728-72873778	HCM	heart:	n/a
17	chr9:72873728-72873778	SK-N-MC	brain:	n/a
18	chr9:72873728-72873778	CMK	blood:	n/a
19	chr9:72873728-72873778	PFSK-1	brain:	n/a
20	chr9:72873728-72873778	HEEpiC	esophagus:	n/a
21	chr9:72873728-72873778	GM12892	blood:	n/a
22	chr9:72873728-72873778	HepG2	liver:	n/a
23	chr9:72873728-72873778	SK-N-SH	brain:	n/a
24	chr9:72873728-72873778	H1-hESC	embryonic stem cell:	embryo
25	chr9:72873728-72873778	NT2-D1	testis:	n/a
26	chr9:72873728-72873778	AG04449	skin:	fetal
27	chr9:72873728-72873778	SKMC	muscle:	n/a
28	chr9:72873728-72873778	BJ	skin:	n/a
29	chr9:72873728-72873778	HRCEpiC	kidney:	n/a
30	chr9:72873728-72873778	LNCaP	prostate:	n/a
31	chr9:72873728-72873778	PANC-1	pancreas:	n/a
32	chr9:72873728-72873778	ovcar-3	ovarian:	n/a
33	chr9:72873728-72873778	Caco-2	colon:	n/a
34	chr9:72873728-72873778	Hepatocyte	liver:	n/a
35	chr9:72873728-72873778	PrEC	prostate:	n/a
36	chr9:72873728-72873778	AG10803	skin:	n/a
37	chr9:72873728-72873778	HPAEpiC	pulmonary alveolar:	n/a
38	chr9:72873728-72873778	HRE	kidney:	n/a
39	chr9:72873728-72873778	SAEC	small airway:	n/a
40	chr9:72873728-72873778	ProgFib	skin:	n/a
41	chr9:72873728-72873778	HCF	heart:	n/a
42	chr9:72873728-72873778	Jurkat	blood:	n/a
43	chr9:72873728-72873778	HNPCEpiC	eye:	n/a
44	chr9:72873728-72873778	AG04450	lung:	fetal
45	chr9:72873728-72873778	RPTEC	kidney:	n/a
46	chr9:72873728-72873778	AG09309	skin:	n/a
47	chr9:72873728-72873778	ECC-1	luminal epithelium:	n/a
48	chr9:72873728-72873778	IMR90	lung:	fetal
49	chr9:72873728-72873778	HUVEC	blood vessel:	n/a
50	chr9:72873728-72873778	K562	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:72872890..72875231-chr9:73027091..73030195,4	K562	blood:
2	chr19:50083124..50083902-chr9:72873392..72874324,2	Hela-S3	cervix:
3	chr3:57678149..57678816-chr9:72873480..72874476,2	Hela-S3	cervix:
4	chr16:87426140..87426868-chr9:72873483..72874472,2	Hela-S3	cervix:
5	chr15:70388787..70390778-chr9:72873616..72875278,2	MCF-7	breast:
6	chr1:11968045..11968807-chr9:72873530..72874374,2	HCT-116	colon:
7	chr17:81037128..81037954-chr9:72873521..72874052,2	HCT-116	colon:
8	chr12:104531449..104532221-chr9:72873633..72874142,2	Hela-S3	cervix:
9	chr9:4298313..4298905-chr9:72873435..72874413,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLF9-3	chr9:72873312-72873790	NONHSAT131808

Variant related genes	Relation type
SMC5	TF binding region
SMC5	CpG island
ENSG00000176845	Chromatin interaction
ENSG00000107249	Chromatin interaction
ENSG00000119138	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000140332	Chromatin interaction
ENSG00000140941	Chromatin interaction
ENSG00000174839	Chromatin interaction
ENSG00000142546	Chromatin interaction
ENSG00000120837	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10114223	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780924	1.00[ASN][1000 genomes]
rs10868800	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10868810	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142348	0.86[EUR][1000 genomes]
rs11142364	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142365	1.00[ASN][1000 genomes]
rs11142372	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142375	0.81[EUR][1000 genomes]
rs11142377	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142379	1.00[ASN][1000 genomes]
rs11142380	1.00[ASN][1000 genomes]
rs11142381	1.00[ASN][1000 genomes]
rs11521805	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11795149	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180080	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180084	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180089	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180097	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180100	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180110	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1180113	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180119	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180134	0.90[EUR][1000 genomes]
rs1183311	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11999862	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052678	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888155	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927094	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927097	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927114	0.81[EUR][1000 genomes]
rs1927123	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927138	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927140	1.00[ASN][1000 genomes]
rs1927141	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927145	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927146	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148854	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148855	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182733	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209781	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225128	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309601	0.81[EUR][1000 genomes]
rs2309637	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309641	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309645	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309646	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871297	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744587	1.00[ASN][1000 genomes]
rs4744985	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66524845	0.81[EUR][1000 genomes]
rs66756859	0.86[EUR][1000 genomes]
rs7020575	0.81[EUR][1000 genomes]
rs7042675	1.00[ASN][1000 genomes]
rs72712293	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712300	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341691	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848955	0.81[EUR][1000 genomes]
rs7865289	0.81[EUR][1000 genomes]
rs9410662	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943532	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943535	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][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	chr9:72872200-72873800	Flanking Active TSS	NH-A	brain
8	chr9:72872200-72874800	Active TSS	Fetal Muscle Trunk	muscle
9	chr9:72872600-72875000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:72872600-72875000	Active TSS	HSMMtube	muscle
11	chr9:72872600-72875600	Active TSS	Brain Cingulate Gyrus	brain
12	chr9:72872800-72873800	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr9:72872800-72873800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr9:72872800-72873800	Active TSS	Brain Germinal Matrix	brain
15	chr9:72872800-72873800	Flanking Active TSS	HUVEC	blood vessel
16	chr9:72872800-72874400	Active TSS	Brain Anterior Caudate	brain
17	chr9:72872800-72874400	Active TSS	Stomach Mucosa	stomach
18	chr9:72872800-72875000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:72872800-72875000	Active TSS	Fetal Intestine Large	intestine
20	chr9:72872800-72875000	Active TSS	Psoas Muscle	Psoas
21	chr9:72872800-72875200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:72872800-72875400	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr9:72872800-72876200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr9:72873000-72873800	Flanking Active TSS	Fetal Thymus	thymus
25	chr9:72873000-72873800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr9:72873000-72874200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:72873000-72874400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr9:72873000-72874400	Active TSS	Fetal Brain Female	brain
29	chr9:72873000-72874400	Active TSS	Thymus	Thymus
30	chr9:72873000-72874600	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr9:72873000-72874600	Active TSS	Brain Hippocampus Middle	brain
32	chr9:72873000-72874600	Active TSS	Brain Substantia Nigra	brain
33	chr9:72873000-72874800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:72873000-72874800	Active TSS	Esophagus	oesophagus
35	chr9:72873000-72875000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:72873000-72875000	Active TSS	Duodenum Mucosa	Duodenum
37	chr9:72873000-72875000	Active TSS	Left Ventricle	heart
38	chr9:72873000-72875000	Active TSS	Right Ventricle	heart
39	chr9:72873000-72875400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr9:72873000-72875400	Active TSS	Fetal Kidney	kidney
41	chr9:72873000-72875400	Active TSS	A549	lung
42	chr9:72873000-72876000	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr9:72873200-72873800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:72873200-72873800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr9:72873200-72874000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:72873200-72874400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr9:72873200-72874400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr9:72873200-72874400	Active TSS	Liver	Liver
49	chr9:72873200-72874600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr9:72873200-72874800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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