Variant report

Variant	rs1180094
Chromosome Location	chr9:72871430-72871431
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 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	ZMIZ1	chr9:72870953-72871605	K562	blood:	n/a	n/a
10	TBP	chr9:72870891-72871443	K562	blood:	n/a	n/a
11	POLR2A	chr9:72871148-72871595	MCF10A-Er-Src	breast:	n/a	n/a
12	ELF1	chr9:72871089-72871530	K562	blood:	n/a	chr9:72871336-72871349
13	POLR2A	chr9:72870881-72871451	K562	blood:	n/a	n/a
14	MYC	chr9:72870984-72871441	K562	blood:	n/a	n/a
15	POLR2A	chr9:72870291-72877116	IMR90	lung:	n/a	n/a
16	GATA1	chr9:72870750-72871583	K562	blood:	n/a	n/a
17	MAZ	chr9:72870978-72871451	K562	blood:	n/a	n/a
18	RCOR1	chr9:72870727-72871485	K562	blood:	n/a	n/a
19	TEAD4	chr9:72870915-72871618	K562	blood:	n/a	n/a
20	POLR2A	chr9:72870997-72871571	U87	brain:	n/a	n/a
21	ARID3A	chr9:72870997-72871503	K562	blood:	n/a	n/a
22	MAZ	chr9:72870647-72871810	IMR90	lung:	n/a	n/a
23	POLR2A	chr9:72871014-72871577	HUVEC	blood vessel:	n/a	n/a
24	TCF12	chr9:72870976-72871718	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr9:72871359-72871455	ProgFib	skin:	n/a	n/a
26	TBL1XR1	chr9:72871074-72871448	K562	blood:	n/a	n/a
27	FOS	chr9:72871220-72871475	MCF10A-Er-Src	breast:	n/a	n/a
28	IRF1	chr9:72870700-72871551	K562	blood:	n/a	n/a
29	JUND	chr9:72870954-72871580	K562	blood:	n/a	n/a
30	CBX3	chr9:72870944-72871522	K562	blood:	n/a	n/a
31	TAL1	chr9:72870928-72871644	K562	blood:	n/a	n/a
32	CEBPD	chr9:72870900-72871453	K562	blood:	n/a	n/a
33	POLR2A	chr9:72870978-72871451	K562	blood:	n/a	n/a
34	RCOR1	chr9:72870938-72871503	K562	blood:	n/a	n/a
35	POLR2A	chr9:72870524-72871581	MCF10A-Er-Src	breast:	n/a	n/a
36	TAF1	chr9:72871099-72871560	SK-N-SH	brain:	n/a	n/a

No data

(count:3 , 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	chr9:72871186..72872849-chr9:73028190..73030062,2	K562	blood:

No data

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

Extended variants
information (count: 144 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10116549	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10117899	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125454	0.83[EUR][1000 genomes]
rs10126027	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10780870	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780871	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780924	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs10868741	0.84[AFR][1000 genomes]
rs10868742	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868800	1.00[CHB][hapmap]
rs10868808	0.89[YRI][hapmap]
rs1112937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11141917	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142242	0.81[AFR][1000 genomes]
rs11142348	1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11142363	0.96[YRI][hapmap]
rs11142365	0.95[EUR][1000 genomes]
rs11142367	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11142368	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11142370	0.96[YRI][hapmap]
rs11142371	0.82[AFR][1000 genomes]
rs11142373	0.96[YRI][hapmap]
rs11142374	0.80[AFR][1000 genomes]
rs11142375	0.88[ASN][1000 genomes]
rs11142377	1.00[CHB][hapmap]
rs11142379	0.93[CEU][hapmap];0.95[EUR][1000 genomes]
rs11142380	0.95[EUR][1000 genomes]
rs11142381	0.95[EUR][1000 genomes]
rs1180079	0.88[AFR][1000 genomes]
rs1180081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1180083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180087	0.94[AFR][1000 genomes]
rs1180088	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180089	1.00[CHB][hapmap]
rs1180091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180098	0.94[AFR][1000 genomes]
rs1180099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180100	1.00[CHB][hapmap]
rs1180101	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1180103	0.88[AFR][1000 genomes]
rs1180104	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1180106	0.94[AFR][1000 genomes]
rs1180107	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1180110	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs1180111	0.97[EUR][1000 genomes]
rs1180112	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs1180114	0.82[AFR][1000 genomes]
rs1180117	0.95[YRI][hapmap];0.80[AFR][1000 genomes]
rs1180118	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1180120	0.80[AFR][1000 genomes]
rs1180122	0.96[YRI][hapmap]
rs1180124	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs1180126	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1180127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180128	0.86[AFR][1000 genomes]
rs1180132	0.80[AFR][1000 genomes]
rs1180133	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs11998951	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs12006212	0.96[YRI][hapmap]
rs12115787	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12156606	1.00[YRI][hapmap]
rs12349698	0.90[AMR][1000 genomes]
rs12377677	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12380844	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17051515	0.80[ASN][1000 genomes]
rs17454349	0.80[ASN][1000 genomes]
rs17454433	0.80[ASN][1000 genomes]
rs17526808	0.80[ASN][1000 genomes]
rs1887451	0.83[EUR][1000 genomes]
rs1927096	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927100	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927101	0.80[ASN][1000 genomes]
rs1927118	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1927124	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927130	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927132	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927133	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927134	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927135	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927136	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1927144	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1927146	0.84[YRI][hapmap]
rs1986067	0.89[ASN][1000 genomes]
rs2026137	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2148857	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148863	0.83[EUR][1000 genomes]
rs2148866	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2148867	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182734	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182737	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182738	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182741	1.00[ASN][1000 genomes]
rs2309634	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309645	1.00[CHB][hapmap]
rs2479033	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2768643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2768644	0.88[AFR][1000 genomes]
rs2768645	0.93[AFR][1000 genomes]
rs2768646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2773362	0.88[AFR][1000 genomes]
rs2773363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773366	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871293	0.96[YRI][hapmap]
rs4384045	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449855	0.96[YRI][hapmap]
rs4744591	0.92[AFR][1000 genomes]
rs4744989	0.92[AMR][1000 genomes]
rs4744993	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744999	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5019539	0.80[ASN][1000 genomes]
rs58720670	0.82[AFR][1000 genomes]
rs6560015	0.80[ASN][1000 genomes]
rs6560016	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6560018	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66524845	0.92[ASN][1000 genomes]
rs66756859	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs68171482	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7019147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024117	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024812	0.80[ASN][1000 genomes]
rs7034322	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7043171	1.00[CHB][hapmap]
rs7047789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73454795	0.82[AFR][1000 genomes]
rs7852005	0.82[AFR][1000 genomes]
rs7853298	0.83[EUR][1000 genomes]
rs7854735	0.84[AFR][1000 genomes]
rs7858988	0.96[YRI][hapmap]
rs7860729	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7868564	0.92[AFR][1000 genomes]
rs7869429	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871674	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs943534	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943535	1.00[CHB][hapmap]
rs943536	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs943540	0.80[YRI][hapmap]

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	chr9:72870200-72871600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:72870200-72872200	Enhancers	Dnd41	blood
7	chr9:72870200-72872800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr9:72870400-72871600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:72870400-72871600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr9:72870400-72871600	Enhancers	HepG2	liver
11	chr9:72870400-72871800	Flanking Active TSS	Fetal Lung	lung
12	chr9:72870400-72871800	Flanking Active TSS	NH-A	brain
13	chr9:72870400-72872000	Flanking Active TSS	HMEC	breast
14	chr9:72870400-72872200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr9:72870400-72873000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:72870400-72873600	Flanking Active TSS	Osteobl	bone
17	chr9:72870400-72874800	Active TSS	Right Atrium	heart
18	chr9:72870600-72871800	Active TSS	Ovary	ovary
19	chr9:72870600-72871800	Flanking Active TSS	HSMM	muscle
20	chr9:72870600-72871800	Flanking Active TSS	HUVEC	blood vessel
21	chr9:72870600-72872400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr9:72870600-72872400	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr9:72870600-72872800	Enhancers	Fetal Brain Female	brain
24	chr9:72870600-72875000	Active TSS	Aorta	Aorta
25	chr9:72870800-72871600	Active TSS	Pancreas	Pancrea
26	chr9:72870800-72871800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:72870800-72871800	Active TSS	Fetal Muscle Trunk	muscle
28	chr9:72870800-72871800	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr9:72870800-72872000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:72870800-72872000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr9:72870800-72872000	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr9:72870800-72872000	Flanking Active TSS	NHEK	skin
33	chr9:72870800-72875200	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr9:72871000-72871600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:72871000-72871600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:72871000-72871600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr9:72871000-72871600	Flanking Active TSS	Fetal Intestine Large	intestine
38	chr9:72871000-72871600	Active TSS	Left Ventricle	heart
39	chr9:72871000-72871800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:72871000-72871800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:72871000-72871800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:72871000-72871800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:72871000-72871800	Flanking Active TSS	Fetal Stomach	stomach
44	chr9:72871000-72872000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr9:72871000-72872000	Flanking Active TSS	HSMMtube	muscle
46	chr9:72871000-72872600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:72871000-72872600	Active TSS	Fetal Brain Male	brain
48	chr9:72871000-72873200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr9:72871000-72876200	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr9:72871200-72871600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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