Variant report

Variant	rs4606121
Chromosome Location	chr9:72878030-72878031
allele	C/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	RELA	chr9:72877084-72878130	GM12878	blood:	n/a	n/a
2	CEBPB	chr9:72877872-72878671	IMR90	lung:	n/a	chr9:72878026-72878037 chr9:72878279-72878292
3	SPI1	chr9:72877826-72878090	GM12891	blood:	n/a	n/a
4	NFIC	chr9:72877145-72878106	GM12878	blood:	n/a	chr9:72877904-72877921 chr9:72877904-72877920
5	ZNF384	chr9:72877744-72878055	GM12878	blood:	n/a	n/a
6	CEBPB	chr9:72877869-72878192	HepG2	liver:	n/a	chr9:72878026-72878037
7	FOS	chr9:72878018-72878669	MCF10A-Er-Src	breast:	n/a	n/a
8	ATF2	chr9:72877254-72878068	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72877983..72879807-chr9:72885567..72887477,3	K562	blood:

Variant related genes	Relation type
SMC5-AS1	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10491653	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1073540	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12683706	0.87[AMR][1000 genomes]
rs12683986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12684301	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12684987	0.87[AMR][1000 genomes]
rs12685322	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12685441	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12685491	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12685534	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12686312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12686573	0.87[AMR][1000 genomes]
rs12686584	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12686850	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17051690	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17051696	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17052443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17052748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17053503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17088796	0.87[AMR][1000 genomes]
rs17088840	0.87[AMR][1000 genomes]
rs17088889	0.87[AMR][1000 genomes]
rs17088905	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1927116	0.87[AMR][1000 genomes]
rs1927117	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1927119	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1927142	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1927143	0.82[ASN][1000 genomes]
rs1927148	0.86[ASN][1000 genomes]
rs1927150	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2148853	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2148865	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2182732	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296772	0.87[AMR][1000 genomes]
rs2296773	0.87[AMR][1000 genomes]
rs2871295	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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];0.99[ASN][1000 genomes]
rs35188046	0.87[AMR][1000 genomes]
rs35508139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3739773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3739774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4069793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4287005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4410968	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4439194	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4495496	0.87[AMR][1000 genomes]
rs4596711	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4602958	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4610818	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4621877	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56735283	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56860643	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57048128	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs57398306	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57477024	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58219953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58662316	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58948879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58969772	0.81[AMR][1000 genomes]
rs58976318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59010963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59444215	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59546243	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59589460	0.87[AMR][1000 genomes]
rs59619263	0.87[AMR][1000 genomes]
rs59960592	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59976188	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60049462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60391643	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60458589	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61092050	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61265226	0.87[AMR][1000 genomes];0.81[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];0.95[ASN][1000 genomes]
rs753022	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs753023	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs943540	0.85[ASN][1000 genomes]
rs954808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[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:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72874800-72878600	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr9:72874800-72879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr9:72875000-72879200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:72875000-72879400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr9:72875000-72949800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:72875200-72878600	Enhancers	Small Intestine	intestine
7	chr9:72875200-72901400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr9:72875400-72879200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:72875400-72879400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:72875400-72906200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:72875600-72878600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr9:72875600-72878600	Enhancers	Colon Smooth Muscle	Colon
13	chr9:72875600-72879200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:72875800-72878400	Enhancers	Fetal Brain Female	brain
15	chr9:72875800-72878600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr9:72875800-72878600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr9:72875800-72878800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:72875800-72879200	Weak transcription	Fetal Kidney	kidney
19	chr9:72875800-72884200	Weak transcription	Lung	lung
20	chr9:72876000-72878200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr9:72876000-72878400	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr9:72876000-72878400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr9:72876000-72878600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr9:72876000-72879800	Weak transcription	Left Ventricle	heart
25	chr9:72876000-72882400	Weak transcription	Fetal Intestine Small	intestine
26	chr9:72876000-72882400	Strong transcription	Fetal Muscle Trunk	muscle
27	chr9:72876000-72883200	Strong transcription	Placenta	Placenta
28	chr9:72876000-72887600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:72876000-72898200	Weak transcription	Fetal Brain Male	brain
30	chr9:72876000-72906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:72876200-72878400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr9:72876200-72878800	Genic enhancers	HSMMtube	muscle
33	chr9:72876200-72879200	Weak transcription	Adipose Nuclei	Adipose
34	chr9:72876200-72880200	Strong transcription	Primary hematopoietic stem cells	blood
35	chr9:72876400-72878200	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr9:72876400-72878600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr9:72876400-72879000	Weak transcription	Right Atrium	heart
38	chr9:72876400-72879200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr9:72876400-72879200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr9:72876400-72879400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr9:72876400-72879600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr9:72876400-72879800	Weak transcription	Pancreas	Pancrea
43	chr9:72876400-72880400	Strong transcription	Fetal Intestine Large	intestine
44	chr9:72876400-72884200	Weak transcription	Esophagus	oesophagus
45	chr9:72876400-72884200	Weak transcription	Fetal Stomach	stomach
46	chr9:72876400-72886200	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr9:72876400-72886600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr9:72876400-72889200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:72876400-72916800	Weak transcription	Colonic Mucosa	Colon
50	chr9:72876400-72939400	Weak transcription	Spleen	Spleen

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