Variant report

Variant	rs1180093
Chromosome Location	chr9:72871355-72871356
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:46)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:46 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr9:72870903-72871613	K562	blood:	n/a	n/a
2	EP300	chr9:72870813-72871707	K562	blood:	n/a	n/a
3	POLR2A	chr9:72871165-72871536	SK-N-SH	brain:	n/a	n/a
4	STAT3	chr9:72871335-72871531	MCF10A-Er-Src	breast:	n/a	n/a
5	TRIM28	chr9:72870877-72871433	K562	blood:	n/a	n/a
6	TEAD4	chr9:72870879-72871601	K562	blood:	n/a	n/a
7	FOS	chr9:72871179-72871474	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr9:72870997-72871565	U87	brain:	n/a	n/a
9	UBTF	chr9:72870933-72871415	K562	blood:	n/a	n/a
10	ZMIZ1	chr9:72870953-72871605	K562	blood:	n/a	n/a
11	TBP	chr9:72870891-72871443	K562	blood:	n/a	n/a
12	POLR2A	chr9:72871148-72871595	MCF10A-Er-Src	breast:	n/a	n/a
13	ELF1	chr9:72871089-72871530	K562	blood:	n/a	chr9:72871336-72871349
14	CEBPD	chr9:72870876-72871412	K562	blood:	n/a	n/a
15	POLR2A	chr9:72870881-72871451	K562	blood:	n/a	n/a
16	MYC	chr9:72870984-72871441	K562	blood:	n/a	n/a
17	POLR2A	chr9:72870291-72877116	IMR90	lung:	n/a	n/a
18	ATF1	chr9:72871016-72871379	K562	blood:	n/a	n/a
19	GATA1	chr9:72870750-72871583	K562	blood:	n/a	n/a
20	STAT5A	chr9:72870944-72871426	K562	blood:	n/a	n/a
21	POLR2A	chr9:72870840-72871411	K562	blood:	n/a	n/a
22	MAZ	chr9:72870978-72871451	K562	blood:	n/a	n/a
23	CEBPB	chr9:72871081-72871367	K562	blood:	n/a	n/a
24	RCOR1	chr9:72870727-72871485	K562	blood:	n/a	n/a
25	TEAD4	chr9:72870915-72871618	K562	blood:	n/a	n/a
26	POLR2A	chr9:72870997-72871571	U87	brain:	n/a	n/a
27	ARID3A	chr9:72870997-72871503	K562	blood:	n/a	n/a
28	MAZ	chr9:72870647-72871810	IMR90	lung:	n/a	n/a
29	POLR2A	chr9:72871014-72871577	HUVEC	blood vessel:	n/a	n/a
30	TCF12	chr9:72870976-72871718	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr9:72871021-72871397	K562	blood:	n/a	n/a
32	TBL1XR1	chr9:72871074-72871448	K562	blood:	n/a	n/a
33	E2F4	chr9:72871220-72871413	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr9:72871220-72871475	MCF10A-Er-Src	breast:	n/a	n/a
35	IRF1	chr9:72870700-72871551	K562	blood:	n/a	n/a
36	POLR2A	chr9:72871282-72871395	HUVEC	blood vessel:	n/a	n/a
37	JUND	chr9:72870954-72871580	K562	blood:	n/a	n/a
38	CBX3	chr9:72870944-72871522	K562	blood:	n/a	n/a
39	MYC	chr9:72871015-72871429	K562	blood:	n/a	n/a
40	TAL1	chr9:72870928-72871644	K562	blood:	n/a	n/a
41	CEBPD	chr9:72870900-72871453	K562	blood:	n/a	n/a
42	POLR2A	chr9:72870978-72871451	K562	blood:	n/a	n/a
43	RCOR1	chr9:72870938-72871503	K562	blood:	n/a	n/a
44	POLR2A	chr9:72870524-72871581	MCF10A-Er-Src	breast:	n/a	n/a
45	TAF1	chr9:72871099-72871560	SK-N-SH	brain:	n/a	n/a
46	PML	chr9:72870955-72871381	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:72871343-72871393	CMK	blood:	n/a
2	chr9:72871343-72871393	Caco-2	colon:	n/a
3	chr9:72871343-72871393	A549	lung:	n/a
4	chr9:72871343-72871393	HEK293	kidney:	embryo
5	chr9:72871343-72871393	GM06990	blood:	n/a
6	chr9:72871343-72871393	GM12892	blood:	n/a
7	chr9:72871343-72871393	HUVEC	blood vessel:	n/a
8	chr9:72871343-72871393	ECC-1	luminal epithelium:	n/a
9	chr9:72871343-72871393	PANC-1	pancreas:	n/a
10	chr9:72871343-72871393	HCM	heart:	n/a
11	chr9:72871343-72871393	Jurkat	blood:	n/a
12	chr9:72871343-72871393	SK-N-SH	brain:	n/a
13	chr9:72871343-72871393	AG04449	skin:	fetal
14	chr9:72871343-72871393	HMEC	breast:	n/a
15	chr9:72871343-72871393	IMR90	lung:	fetal
16	chr9:72871343-72871393	HAEpiC	amniotic membrane:	n/a
17	chr9:72871343-72871393	HRE	kidney:	n/a
18	chr9:72871343-72871393	SK-N-MC	brain:	n/a
19	chr9:72871343-72871393	PrEC	prostate:	n/a
20	chr9:72871343-72871393	AoSMC	blood vessel:	n/a
21	chr9:72871343-72871393	HCPEpiC	choroid plexus:	n/a
22	chr9:72871343-72871393	NH-A	brain:	n/a
23	chr9:72871343-72871393	NT2-D1	testis:	n/a
24	chr9:72871343-72871393	AG09309	skin:	n/a
25	chr9:72871343-72871393	LNCaP	prostate:	n/a
26	chr9:72871343-72871393	K562	blood:	n/a
27	chr9:72871343-72871393	H1-hESC	embryonic stem cell:	embryo
28	chr9:72871343-72871393	ProgFib	skin:	n/a
29	chr9:72871343-72871393	AG10803	skin:	n/a
30	chr9:72871343-72871393	HRPEpiC	eye:	n/a
31	chr9:72871343-72871393	GM12878	blood:	n/a
32	chr9:72871343-72871393	HPAEpiC	pulmonary alveolar:	n/a
33	chr9:72871343-72871393	MCF10A-Er-Src	breast:	n/a
34	chr9:72871343-72871393	Hela-S3	cervix:	n/a
35	chr9:72871343-72871393	HCF	heart:	n/a
36	chr9:72871343-72871393	BE2_C	brain:	n/a
37	chr9:72871343-72871393	HepG2	liver:	n/a
38	chr9:72871343-72871393	HL-60	blood:	n/a
39	chr9:72871343-72871393	NHDF-neo	bronchial:	n/a
40	chr9:72871343-72871393	AG09319	gingival:	n/a
41	chr9:72871343-72871393	Hepatocyte	liver:	n/a
42	chr9:72871343-72871393	ovcar-3	ovarian:	n/a
43	chr9:72871343-72871393	SAEC	small airway:	n/a
44	chr9:72871343-72871393	U87	brain:	n/a
45	chr9:72871343-72871393	SK-N-SH_RA	brain:	n/a
46	chr9:72871343-72871393	GM19239	blood:	n/a
47	chr9:72871343-72871393	NHBE	bronchial:	n/a
48	chr9:72871343-72871393	HRCEpiC	kidney:	n/a
49	chr9:72871343-72871393	MCF-7	breast:	n/a
50	chr9:72871343-72871393	HIPEpiC	eye:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:72726692..72728267-chr9:72871219..72873032,2	MCF-7	breast:
2	chr9:72868452..72871714-chr9:72871997..72874564,6	MCF-7	breast:
3	chr9:72865927..72868229-chr9:72869161..72871391,2	MCF-7	breast:
4	chr9:72871186..72872849-chr9:73028190..73030062,2	K562	blood:

No data

Variant related genes	Relation type
SMC5	TF binding region
SMC5	CpG island
ENSG00000268364	Chromatin interaction
ENSG00000119138	Chromatin interaction
ENSG00000198887	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10868798	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1104709	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11142019	0.88[AMR][1000 genomes]
rs11142141	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11142346	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11142355	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11791792	0.87[AMR][1000 genomes]
rs11793851	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11794396	0.93[AMR][1000 genomes]
rs1180085	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1180090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1180095	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1180109	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1180116	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1180131	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12005243	0.93[AMR][1000 genomes]
rs12338030	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12343885	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12346675	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12352944	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12684881	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2148856	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2183361	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4507832	0.82[AMR][1000 genomes]
rs4744593	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58704591	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62570306	0.87[AMR][1000 genomes]
rs62570318	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7019433	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7023586	0.93[AMR][1000 genomes]
rs7028657	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72712267	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72712271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72712284	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7847861	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7868421	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7873075	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72868000-72872600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:72869200-72871600	Enhancers	Liver	Liver
3	chr9:72869600-72873600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:72869800-72873600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:72870200-72871400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
6	chr9:72870200-72871400	Enhancers	Stomach Mucosa	stomach
7	chr9:72870200-72871600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:72870200-72872200	Enhancers	Dnd41	blood
9	chr9:72870200-72872800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr9:72870400-72871600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:72870400-72871600	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr9:72870400-72871600	Enhancers	HepG2	liver
13	chr9:72870400-72871800	Flanking Active TSS	Fetal Lung	lung
14	chr9:72870400-72871800	Flanking Active TSS	NH-A	brain
15	chr9:72870400-72872000	Flanking Active TSS	HMEC	breast
16	chr9:72870400-72872200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr9:72870400-72873000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:72870400-72873600	Flanking Active TSS	Osteobl	bone
19	chr9:72870400-72874800	Active TSS	Right Atrium	heart
20	chr9:72870600-72871400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:72870600-72871400	Active TSS	Colon Smooth Muscle	Colon
22	chr9:72870600-72871800	Active TSS	Ovary	ovary
23	chr9:72870600-72871800	Flanking Active TSS	HSMM	muscle
24	chr9:72870600-72871800	Flanking Active TSS	HUVEC	blood vessel
25	chr9:72870600-72872400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr9:72870600-72872400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr9:72870600-72872800	Enhancers	Fetal Brain Female	brain
28	chr9:72870600-72875000	Active TSS	Aorta	Aorta
29	chr9:72870800-72871400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:72870800-72871600	Active TSS	Pancreas	Pancrea
31	chr9:72870800-72871800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:72870800-72871800	Active TSS	Fetal Muscle Trunk	muscle
33	chr9:72870800-72871800	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr9:72870800-72872000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:72870800-72872000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr9:72870800-72872000	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr9:72870800-72872000	Flanking Active TSS	NHEK	skin
38	chr9:72870800-72875200	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr9:72871000-72871400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:72871000-72871400	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr9:72871000-72871400	Flanking Active TSS	Colonic Mucosa	Colon
42	chr9:72871000-72871400	Active TSS	Fetal Kidney	kidney
43	chr9:72871000-72871400	Active TSS	Rectal Smooth Muscle	rectum
44	chr9:72871000-72871400	Active TSS	K562	blood
45	chr9:72871000-72871400	Active TSS	NHDF-Ad	bronchial
46	chr9:72871000-72871600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:72871000-72871600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:72871000-72871600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr9:72871000-72871600	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr9:72871000-72871600	Active TSS	Left Ventricle	heart

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