Variant report

Variant	rs4745541
Chromosome Location	chr9:79005263-79005264
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:78999922..79001730-chr9:79004371..79006300,2	MCF-7	breast:
2	chr9:79003083..79006280-chr9:79008607..79011361,3	K562	blood:
3	chr9:79002425..79005766-chr9:79008607..79011361,4	K562	blood:

Variant related genes	Relation type
ENSG00000135002	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10121699	0.81[ASN][1000 genomes]
rs10124695	0.81[ASN][1000 genomes]
rs10781361	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10869767	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10869773	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11144864	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144865	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144866	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11144871	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11144880	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11144898	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12057052	0.82[ASN][1000 genomes]
rs13295433	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13302654	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1535845	0.81[ASN][1000 genomes]
rs1961995	0.83[ASN][1000 genomes]
rs2002423	0.86[ASN][1000 genomes]
rs2251604	0.99[ASN][1000 genomes]
rs2377639	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2490573	0.93[ASN][1000 genomes]
rs2490574	0.81[ASN][1000 genomes]
rs2490576	0.83[ASN][1000 genomes]
rs2490579	0.99[ASN][1000 genomes]
rs2490583	0.86[ASN][1000 genomes]
rs2490584	0.86[ASN][1000 genomes]
rs2490586	0.84[ASN][1000 genomes]
rs2501920	0.81[ASN][1000 genomes]
rs2501922	0.97[ASN][1000 genomes]
rs2501923	0.99[ASN][1000 genomes]
rs2501925	0.97[ASN][1000 genomes]
rs2501927	0.99[ASN][1000 genomes]
rs2501928	0.95[ASN][1000 genomes]
rs2501930	0.82[ASN][1000 genomes]
rs2501932	0.81[ASN][1000 genomes]
rs2501933	0.93[ASN][1000 genomes]
rs2501935	0.93[ASN][1000 genomes]
rs35837300	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3739729	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4372070	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4745544	0.81[ASN][1000 genomes]
rs4745549	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6560517	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7847608	0.81[ASN][1000 genomes]
rs7849239	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7861089	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:78986600-79008400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:78987600-79007800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr9:78988200-79008400	Weak transcription	Brain Substantia Nigra	brain
4	chr9:78988200-79008400	Weak transcription	Fetal Heart	heart
5	chr9:78988600-79007800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:78988600-79008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:78988800-79006000	Weak transcription	Brain Angular Gyrus	brain
8	chr9:78988800-79007200	Weak transcription	Brain Hippocampus Middle	brain
9	chr9:78988800-79008400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:78990000-79005400	Weak transcription	Small Intestine	intestine
11	chr9:78990200-79007800	Weak transcription	Fetal Brain Male	brain
12	chr9:78990200-79008400	Weak transcription	Right Ventricle	heart
13	chr9:78990400-79008200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:78990400-79008400	Weak transcription	Fetal Kidney	kidney
15	chr9:78990600-79005600	Weak transcription	K562	blood
16	chr9:78990600-79008400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:78990600-79008400	Weak transcription	Fetal Lung	lung
18	chr9:78990600-79008400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:78990800-79008400	Weak transcription	NHLF	lung
20	chr9:78992200-79008600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:78995200-79007600	Weak transcription	Gastric	stomach
22	chr9:78995200-79007600	Weak transcription	HMEC	breast
23	chr9:78995200-79007600	Weak transcription	NHEK	skin
24	chr9:78995200-79008400	Weak transcription	Stomach Mucosa	stomach
25	chr9:78995200-79008600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:78996000-79008400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr9:78997000-79007600	Weak transcription	Lung	lung
28	chr9:78997600-79005800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr9:78997600-79008400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:78997800-79008400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:78998400-79008400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:78998800-79007800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:78998800-79008600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr9:78999000-79007600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr9:78999200-79008400	Weak transcription	NH-A	brain
36	chr9:78999400-79008600	Weak transcription	Spleen	Spleen
37	chr9:78999600-79006600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:78999800-79007600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:79000000-79007000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr9:79000200-79007400	Weak transcription	Colonic Mucosa	Colon
41	chr9:79000200-79008400	Weak transcription	Pancreas	Pancrea
42	chr9:79000400-79008400	Weak transcription	Thymus	Thymus
43	chr9:79002000-79008400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:79002600-79007400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr9:79002800-79006400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:79003000-79005800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr9:79003000-79007400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr9:79003000-79007400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:79003000-79007600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr9:79003000-79007800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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