Variant report

Variant	rs1180097
Chromosome Location	chr9:72874869-72874870
allele	A/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	GATA1	chr9:72873523-72874962	PBDE	blood:	n/a	chr9:72874615-72874622 chr9:72874615-72874622 chr9:72874615-72874622 chr9:72874561-72874570
2	CEBPB	chr9:72874863-72875276	MCF-7	breast:	n/a	chr9:72875076-72875087
3	POLR2A	chr9:72872279-72874875	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:72873203-72875053	GM12878	blood:	n/a	n/a
5	POLR2A	chr9:72870291-72877116	IMR90	lung:	n/a	n/a
6	SETDB1	chr9:72874773-72875448	U2OS	brain:	n/a	n/a
7	CEBPB	chr9:72874788-72875255	HepG2	liver:	n/a	chr9:72875076-72875087
8	MAZ	chr9:72873009-72875061	IMR90	lung:	n/a	chr9:72874255-72874264
9	CHD1	chr9:72871992-72876758	IMR90	lung:	n/a	chr9:72873802-72873812
10	CHD1	chr9:72873223-72874909	GM12878	blood:	n/a	chr9:72873802-72873812
11	SIN3AK20	chr9:72873139-72874896	MCF-7	breast:	n/a	n/a
12	HA-E2F1	chr9:72873233-72875530	MCF-7	breast:	n/a	chr9:72873896-72873911 chr9:72873792-72873804 chr9:72873909-72873919 chr9:72873843-72873853 chr9:72873841-72873850 chr9:72873858-72873869 chr9:72874227-72874237
13	POLR2A	chr9:72874798-72875208	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:72872890..72875231-chr9:73027091..73030195,4	K562	blood:
2	chr9:72874733..72877104-chr9:72888484..72890137,2	K562	blood:
3	chr15:70388787..70390778-chr9:72873616..72875278,2	MCF-7	breast:
4	chr9:72373387..72376208-chr9:72873924..72875696,2	K562	blood:

Variant related genes	Relation type
SMC5-AS1	TF binding region
ENSG00000188647	Chromatin interaction
ENSG00000140332	Chromatin interaction
ENSG00000119138	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10114223	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10735584	0.81[AMR][1000 genomes]
rs10780924	1.00[ASN][1000 genomes]
rs10868800	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10868810	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142348	0.95[EUR][1000 genomes]
rs11142364	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142365	1.00[ASN][1000 genomes]
rs11142372	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142375	0.91[EUR][1000 genomes]
rs11142377	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11795149	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180080	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180084	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180089	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180100	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180110	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1180111	0.82[AFR][1000 genomes]
rs1180113	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180119	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1180134	1.00[EUR][1000 genomes]
rs1183311	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11999862	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052678	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888155	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927094	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927097	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927108	0.81[AMR][1000 genomes]
rs1927109	0.81[AMR][1000 genomes]
rs1927112	0.87[AMR][1000 genomes]
rs1927114	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1927123	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927138	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927140	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927141	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927145	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1927146	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148854	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148855	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182733	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209781	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2225128	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309601	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2309637	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309641	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309645	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309646	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2479033	0.82[AFR][1000 genomes]
rs2871297	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744587	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744985	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66524845	0.91[EUR][1000 genomes]
rs66756859	0.95[EUR][1000 genomes]
rs7020575	0.86[EUR][1000 genomes]
rs7042675	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72712300	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341691	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848955	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7865289	0.86[EUR][1000 genomes]
rs9410662	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943532	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943533	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs943535	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[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	chr9:72870600-72875000	Active TSS	Aorta	Aorta
2	chr9:72870800-72875200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr9:72871000-72876200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr9:72871800-72875200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:72872000-72875000	Active TSS	Pancreas	Pancrea
6	chr9:72872600-72875000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr9:72872600-72875000	Active TSS	HSMMtube	muscle
8	chr9:72872600-72875600	Active TSS	Brain Cingulate Gyrus	brain
9	chr9:72872800-72875000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:72872800-72875000	Active TSS	Fetal Intestine Large	intestine
11	chr9:72872800-72875000	Active TSS	Psoas Muscle	Psoas
12	chr9:72872800-72875200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:72872800-72875400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr9:72872800-72876200	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr9:72873000-72875000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:72873000-72875000	Active TSS	Duodenum Mucosa	Duodenum
17	chr9:72873000-72875000	Active TSS	Left Ventricle	heart
18	chr9:72873000-72875000	Active TSS	Right Ventricle	heart
19	chr9:72873000-72875400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:72873000-72875400	Active TSS	Fetal Kidney	kidney
21	chr9:72873000-72875400	Active TSS	A549	lung
22	chr9:72873000-72876000	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr9:72873200-72875000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr9:72873200-72875000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:72873200-72875000	Active TSS	Gastric	stomach
26	chr9:72873200-72875000	Active TSS	Ovary	ovary
27	chr9:72873200-72875200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr9:72873200-72875200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:72873200-72875200	Active TSS	Brain Angular Gyrus	brain
30	chr9:72873400-72875000	Active TSS	Fetal Lung	lung
31	chr9:72873400-72875000	Active TSS	Placenta Amnion	Placenta Amnion
32	chr9:72873400-72875200	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr9:72873400-72875200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:72873400-72875400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr9:72873400-72875400	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr9:72873400-72875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr9:72873400-72875400	Active TSS	NHDF-Ad	bronchial
38	chr9:72873400-72876000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr9:72873600-72875000	Active TSS	H1 Cell Line	embryonic stem cell
40	chr9:72873600-72875000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:72873600-72875000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:72873600-72875000	Active TSS	Fetal Intestine Small	intestine
43	chr9:72873600-72875000	Active TSS	Stomach Smooth Muscle	stomach
44	chr9:72873600-72875200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:72873600-72875200	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr9:72873600-72875200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr9:72873600-72875200	Active TSS	HMEC	breast
48	chr9:72873600-72875200	Active TSS	HSMM	muscle
49	chr9:72873600-72875200	Active TSS	K562	blood
50	chr9:72873600-72875400	Active TSS	HUES48 Cell Line	embryonic stem cell

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