Variant report

Variant	rs4589362
Chromosome Location	chr12:48478664-48478665
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	SPI1	chr12:48478601-48478989	GM12891	blood:	n/a	n/a
2	SPI1	chr12:48478648-48478980	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000226138	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1018973	0.89[EUR][1000 genomes]
rs10492080	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10875742	0.88[ASN][1000 genomes]
rs11609399	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11612578	0.85[EUR][1000 genomes]
rs11612970	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11613485	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11613781	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12580764	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12581972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476608	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17122611	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17122612	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17122613	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17122651	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1859441	0.86[EUR][1000 genomes]
rs1968071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1990029	0.81[EUR][1000 genomes]
rs2286022	0.84[EUR][1000 genomes]
rs3742074	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4075913	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4141065	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4293182	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760611	0.86[EUR][1000 genomes]
rs4760614	0.89[EUR][1000 genomes]
rs4760615	0.87[EUR][1000 genomes]
rs4760618	0.84[EUR][1000 genomes]
rs4760620	0.85[EUR][1000 genomes]
rs4760677	0.89[EUR][1000 genomes]
rs4760683	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57054831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57380031	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57655233	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58046797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58331734	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59766465	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60567660	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60629297	0.84[EUR][1000 genomes]
rs60681522	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580647	0.82[EUR][1000 genomes]
rs6580651	0.89[EUR][1000 genomes]
rs6580656	0.84[EUR][1000 genomes]
rs7133249	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs726354	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72644841	0.85[EUR][1000 genomes]
rs72644842	0.89[EUR][1000 genomes]
rs72644843	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72644844	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72644845	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72644846	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72644847	0.92[EUR][1000 genomes]
rs7296913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7305954	0.81[EUR][1000 genomes]
rs7310579	0.87[EUR][1000 genomes]
rs7312326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315258	0.84[EUR][1000 genomes]
rs7485824	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs757556	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7957764	0.87[EUR][1000 genomes]
rs7959755	0.89[EUR][1000 genomes]
rs7963934	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967762	0.82[EUR][1000 genomes]
rs7969749	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7971668	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs879242	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9651993	0.81[EUR][1000 genomes]
rs9805048	0.81[EUR][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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4589362	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
4	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:48454600-48478800	Weak transcription	Pancreas	Pancrea
8	chr12:48457400-48482000	Weak transcription	Right Ventricle	heart
9	chr12:48459200-48479000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:48464600-48489400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:48464800-48482400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:48465000-48478800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:48465000-48478800	Weak transcription	Aorta	Aorta
14	chr12:48465000-48487400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:48466200-48481400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr12:48466800-48478800	Weak transcription	Esophagus	oesophagus
17	chr12:48468200-48478800	Weak transcription	HepG2	liver
18	chr12:48468400-48478800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:48468400-48481400	Weak transcription	NHDF-Ad	bronchial
20	chr12:48468400-48482200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:48468400-48482200	Weak transcription	Brain Substantia Nigra	brain
22	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:48468800-48478800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:48468800-48482800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:48470200-48497600	Weak transcription	Fetal Heart	heart
27	chr12:48470800-48492800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:48471400-48492000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:48472200-48489400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:48472400-48492000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr12:48472600-48486400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:48472600-48490200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr12:48472600-48490200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:48472600-48493600	Strong transcription	Fetal Thymus	thymus
35	chr12:48472800-48483200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:48472800-48493800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:48473000-48494800	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr12:48473200-48478800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:48473200-48482600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr12:48473200-48486200	Strong transcription	Placenta	Placenta
41	chr12:48473200-48492000	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:48473600-48490000	Strong transcription	Primary T cells from cord blood	blood
43	chr12:48473600-48495400	Strong transcription	Dnd41	blood
44	chr12:48473800-48480000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr12:48473800-48491600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr12:48473800-48492800	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr12:48474000-48479600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:48474000-48484600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:48474000-48485600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:48474000-48493000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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