Variant report

Variant	rs1180095
Chromosome Location	chr9:72873472-72873473
allele	C/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	POLR2A	chr9:72873200-72874273	GM12892	blood:	n/a	n/a
2	POLR2A	chr9:72873239-72874366	HCT-116	colon:	n/a	n/a
3	MXI1	chr9:72873235-72874496	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:72873412-72874835	GM12878	blood:	n/a	n/a
5	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
6	POLR2A	chr9:72873155-72874555	Hela-S3	cervix:	n/a	n/a
7	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
8	MAX	chr9:72873058-72874712	HCT-116	colon:	n/a	chr9:72874255-72874264
9	MAX	chr9:72873069-72874808	ECC-1	luminal epithelium:	n/a	chr9:72874255-72874264
10	MAZ	chr9:72873421-72874456	HepG2	liver:	n/a	chr9:72874255-72874264
11	POLR2A	chr9:72873437-72874180	PANC-1	pancreas:	n/a	n/a
12	E2F6	chr9:72873315-72874130	A549	lung:	n/a	chr9:72873896-72873911 chr9:72873792-72873804 chr9:72873909-72873919 chr9:72873843-72873853 chr9:72873841-72873850
13	MAX	chr9:72873096-72874600	ECC-1	luminal epithelium:	n/a	chr9:72874255-72874264
14	YY1	chr9:72873370-72874169	ECC-1	luminal epithelium:	n/a	chr9:72873796-72873807 chr9:72873901-72873912
15	MBD4	chr9:72873365-72873893	HepG2	liver:	n/a	n/a
16	CHD2	chr9:72873367-72874354	K562	blood:	n/a	chr9:72873802-72873812
17	POLR2A	chr9:72872858-72874429	U87	brain:	n/a	n/a
18	MYBL2	chr9:72873327-72874066	HepG2	liver:	n/a	n/a
19	TFAP2C	chr9:72873172-72874542	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr9:72873448-72874286	K562	blood:	n/a	n/a
21	BATF	chr9:72873122-72873481	GM12878	blood:	n/a	n/a
22	MYC	chr9:72873032-72874620	NB4	blood:	n/a	chr9:72874255-72874264
23	POLR2A	chr9:72872979-72874209	HepG2	liver:	n/a	n/a
24	POU2F2	chr9:72873401-72874176	GM12891	blood:	n/a	chr9:72873796-72873808
25	RELA	chr9:72873238-72874490	GM19099	blood:	n/a	n/a
26	NRF1	chr9:72873391-72874428	GM12878	blood:	n/a	chr9:72873840-72873851 chr9:72873839-72873850 chr9:72873840-72873849 chr9:72873840-72873854 chr9:72873837-72873851
27	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
28	POLR2A	chr9:72873428-72874320	A549	lung:	n/a	n/a
29	POLR2A	chr9:72873463-72874320	U87	brain:	n/a	n/a
30	MAX	chr9:72873114-72874532	A549	lung:	n/a	chr9:72874255-72874264
31	MAZ	chr9:72873179-72874585	K562	blood:	n/a	chr9:72874255-72874264
32	RCOR1	chr9:72873224-72874095	K562	blood:	n/a	n/a
33	POLR2A	chr9:72873463-72874313	U87	brain:	n/a	n/a
34	BCLAF1	chr9:72873088-72874424	GM12878	blood:	n/a	chr9:72873786-72873795 chr9:72873899-72873912
35	CHD2	chr9:72873405-72874577	Hela-S3	cervix:	n/a	chr9:72873802-72873812
36	TAF1	chr9:72873416-72874246	H1-hESC	embryonic stem cell:	n/a	n/a
37	HEY1	chr9:72873049-72873478	HepG2	liver:	n/a	n/a
38	UBTF	chr9:72873135-72874495	K562	blood:	n/a	n/a
39	POLR2A	chr9:72873323-72874700	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr9:72872909-72874290	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr9:72873118-72874334	HL-60	blood:	n/a	n/a
42	POLR2A	chr9:72872279-72874875	HepG2	liver:	n/a	n/a
43	MAX	chr9:72872944-72874679	HepG2	liver:	n/a	chr9:72874255-72874264
44	POLR2A	chr9:72873203-72875053	GM12878	blood:	n/a	n/a
45	POLR2A	chr9:72872969-72874616	GM18505	blood:	n/a	n/a
46	POLR2A	chr9:72873084-72874514	GM18951	blood:	n/a	n/a
47	TAF1	chr9:72873236-72874420	A549	lung:	n/a	n/a
48	POLR2A	chr9:72873413-72874531	HL-60	blood:	n/a	n/a
49	STAT3	chr9:72873160-72873753	GM12878	blood:	n/a	n/a
50	POLR2A	chr9:72873393-72873587	A549	lung:	n/a	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	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
2	lnc-KLF9-3	chr9:72872027-72873730	NONHSAT131810

Variant related genes	Relation type
SMC5	TF binding region
ENSG00000142546	Chromatin interaction
ENSG00000119138	Chromatin interaction
ENSG00000107249	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10868798	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1104709	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11142019	0.85[AMR][1000 genomes]
rs11142141	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11142346	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11142355	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11791792	0.84[AMR][1000 genomes]
rs11793851	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11794396	0.90[AMR][1000 genomes]
rs1180085	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180090	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180093	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1180109	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1180116	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1180131	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12005243	0.90[AMR][1000 genomes]
rs12338030	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12343885	0.90[AMR][1000 genomes]
rs12346675	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12352944	0.90[AMR][1000 genomes]
rs12684881	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2148856	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2183361	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4744593	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58704591	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62570306	0.84[AMR][1000 genomes]
rs62570318	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7019433	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7023586	0.90[AMR][1000 genomes]
rs7028657	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72712267	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72712271	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72712284	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7847861	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7868421	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7873075	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	chr9:72869600-72873600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:72869800-72873600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:72870400-72873600	Flanking Active TSS	Osteobl	bone
4	chr9:72870400-72874800	Active TSS	Right Atrium	heart
5	chr9:72870600-72875000	Active TSS	Aorta	Aorta
6	chr9:72870800-72875200	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr9:72871000-72876200	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr9:72871800-72875200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:72872000-72875000	Active TSS	Pancreas	Pancrea
10	chr9:72872200-72873600	Flanking Active TSS	Fetal Muscle Leg	muscle
11	chr9:72872200-72873600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr9:72872200-72873600	Flanking Active TSS	Stomach Smooth Muscle	stomach
13	chr9:72872200-72873600	Flanking Active TSS	Dnd41	blood
14	chr9:72872200-72873600	Flanking Active TSS	HMEC	breast
15	chr9:72872200-72873600	Flanking Active TSS	NHEK	skin
16	chr9:72872200-72873800	Flanking Active TSS	NH-A	brain
17	chr9:72872200-72874800	Active TSS	Fetal Muscle Trunk	muscle
18	chr9:72872400-72873600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:72872400-72873600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr9:72872400-72873600	Flanking Active TSS	Fetal Intestine Small	intestine
21	chr9:72872400-72873600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr9:72872600-72873600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:72872600-72873600	Flanking Active TSS	NHLF	lung
24	chr9:72872600-72875000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr9:72872600-72875000	Active TSS	HSMMtube	muscle
26	chr9:72872600-72875600	Active TSS	Brain Cingulate Gyrus	brain
27	chr9:72872800-72873600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr9:72872800-72873600	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr9:72872800-72873600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:72872800-72873600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr9:72872800-72873600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:72872800-72873600	Flanking Active TSS	GM12878-XiMat	blood
33	chr9:72872800-72873800	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr9:72872800-72873800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr9:72872800-72873800	Active TSS	Brain Germinal Matrix	brain
36	chr9:72872800-72873800	Flanking Active TSS	HUVEC	blood vessel
37	chr9:72872800-72874400	Active TSS	Brain Anterior Caudate	brain
38	chr9:72872800-72874400	Active TSS	Stomach Mucosa	stomach
39	chr9:72872800-72875000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr9:72872800-72875000	Active TSS	Fetal Intestine Large	intestine
41	chr9:72872800-72875000	Active TSS	Psoas Muscle	Psoas
42	chr9:72872800-72875200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:72872800-72875400	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr9:72872800-72876200	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr9:72873000-72873600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
46	chr9:72873000-72873600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr9:72873000-72873600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr9:72873000-72873600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr9:72873000-72873600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr9:72873000-72873600	Flanking Active TSS	Primary B cells from peripheral blood	blood

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