Variant report

Variant	rs4287005
Chromosome Location	chr9:72870601-72870602
allele	A/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	FOS	chr9:72870452-72870784	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr9:72870486-72870766	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr9:72870457-72870763	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr9:72870291-72877116	IMR90	lung:	n/a	n/a
5	POLR2A	chr9:72870524-72871581	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:72868706..72870705-chr9:73034414..73037199,2	K562	blood:
2	chr9:72868452..72871714-chr9:72871997..72874564,6	MCF-7	breast:
3	chr9:72865927..72868229-chr9:72869161..72871391,2	MCF-7	breast:
4	chr9:72859906..72862605-chr9:72869481..72871220,2	K562	blood:

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

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10491653	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1073540	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12683706	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12683986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12684301	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12684987	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12685322	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12685441	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12685491	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12685534	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12686312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12686573	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12686584	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686850	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17051690	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17051696	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17052443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17052748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17053503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17088796	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17088840	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17088889	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17088905	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1927116	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1927117	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1927119	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1927142	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1927143	0.83[ASN][1000 genomes]
rs1927148	0.87[ASN][1000 genomes]
rs1927150	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2026138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2148853	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2148865	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2182732	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2296772	0.87[AMR][1000 genomes]
rs2296773	0.87[AMR][1000 genomes]
rs2871290	0.80[ASN][1000 genomes]
rs2871295	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3015223	0.87[AMR][1000 genomes]
rs34061327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35188046	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs35508139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3739773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3739774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4069793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4410968	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4439194	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4495496	0.87[AMR][1000 genomes]
rs4596711	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4602958	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4606121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4610818	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4621877	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744982	0.80[ASN][1000 genomes]
rs56735283	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56860643	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57048128	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs57398306	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57477024	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58219953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58662316	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58948879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58969772	0.81[AMR][1000 genomes]
rs58976318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59010963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59189596	0.80[ASN][1000 genomes]
rs59444215	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59546243	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59589460	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59619263	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59960592	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59976188	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60049462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60391643	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60458589	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61092050	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61265226	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61266539	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7046167	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs716535	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs753022	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs753023	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7875348	0.80[ASN][1000 genomes]
rs943540	0.86[ASN][1000 genomes]
rs954808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[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:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72847400-72870800	Weak transcription	Pancreas	Pancrea
2	chr9:72855800-72870800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:72860600-72870800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:72867600-72870800	Weak transcription	Brain Angular Gyrus	brain
5	chr9:72868000-72870800	Weak transcription	Brain Substantia Nigra	brain
6	chr9:72868000-72871200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr9:72868000-72872600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr9:72868400-72870800	Weak transcription	Fetal Stomach	stomach
9	chr9:72868400-72871000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:72869200-72871600	Enhancers	Liver	Liver
11	chr9:72869400-72871000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:72869400-72871000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:72869600-72873600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:72869800-72870800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr9:72869800-72873600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:72870000-72871000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:72870000-72871200	Weak transcription	Psoas Muscle	Psoas
18	chr9:72870200-72870800	Enhancers	NHEK	skin
19	chr9:72870200-72871400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr9:72870200-72871400	Enhancers	Stomach Mucosa	stomach
21	chr9:72870200-72871600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:72870200-72872200	Enhancers	Dnd41	blood
23	chr9:72870200-72872800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr9:72870400-72870800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:72870400-72870800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:72870400-72870800	Enhancers	Brain Anterior Caudate	brain
27	chr9:72870400-72870800	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr9:72870400-72870800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr9:72870400-72870800	Enhancers	Fetal Intestine Small	intestine
30	chr9:72870400-72870800	Active TSS	Fetal Muscle Leg	muscle
31	chr9:72870400-72870800	Active TSS	Stomach Smooth Muscle	stomach
32	chr9:72870400-72870800	Enhancers	NHLF	lung
33	chr9:72870400-72871000	Enhancers	Fetal Brain Male	brain
34	chr9:72870400-72871000	Enhancers	Fetal Intestine Large	intestine
35	chr9:72870400-72871000	Active TSS	HSMMtube	muscle
36	chr9:72870400-72871200	Enhancers	Small Intestine	intestine
37	chr9:72870400-72871600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:72870400-72871600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr9:72870400-72871600	Enhancers	HepG2	liver
40	chr9:72870400-72871800	Flanking Active TSS	Fetal Lung	lung
41	chr9:72870400-72871800	Flanking Active TSS	NH-A	brain
42	chr9:72870400-72872000	Flanking Active TSS	HMEC	breast
43	chr9:72870400-72872200	Enhancers	Placenta Amnion	Placenta Amnion
44	chr9:72870400-72873000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:72870400-72873600	Flanking Active TSS	Osteobl	bone
46	chr9:72870400-72874800	Active TSS	Right Atrium	heart
47	chr9:72870600-72870800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr9:72870600-72870800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:72870600-72870800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:72870600-72870800	Active TSS	Pancreatic Islets	Pancreatic Islet

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