Variant report

Variant	rs72809790
Chromosome Location	chr5:179174053-179174054
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179173901..179176407-chr5:179192308..179193832,2	MCF-7	breast:
2	chr5:179165284..179168030-chr5:179172314..179174869,3	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs41285559	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55793208	1.00[AFR][1000 genomes]
rs55800082	1.00[EUR][1000 genomes]
rs55815501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55915939	1.00[EUR][1000 genomes]
rs55952102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55967209	1.00[EUR][1000 genomes]
rs56030002	1.00[AFR][1000 genomes]
rs56040295	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56093222	1.00[EUR][1000 genomes]
rs60485189	1.00[EUR][1000 genomes]
rs60716268	1.00[EUR][1000 genomes]
rs66465242	0.90[EUR][1000 genomes]
rs66685266	1.00[EUR][1000 genomes]
rs66686562	1.00[EUR][1000 genomes]
rs67211456	1.00[EUR][1000 genomes]
rs67637906	1.00[EUR][1000 genomes]
rs67832593	0.89[EUR][1000 genomes]
rs67879510	1.00[EUR][1000 genomes]
rs67952129	1.00[EUR][1000 genomes]
rs6865507	1.00[EUR][1000 genomes]
rs72807319	1.00[EUR][1000 genomes]
rs72807324	1.00[AFR][1000 genomes]
rs72807328	1.00[EUR][1000 genomes]
rs72807332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72807337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809763	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72809769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72809771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72809772	1.00[AFR][1000 genomes]
rs72809773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72809775	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809785	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809787	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809792	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809794	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809795	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809796	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179161000-179174200	Weak transcription	Esophagus	oesophagus
2	chr5:179161000-179181200	Weak transcription	Aorta	Aorta
3	chr5:179161000-179181600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:179161000-179181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:179161600-179176600	Weak transcription	HSMMtube	muscle
6	chr5:179161800-179174200	Weak transcription	A549	lung
7	chr5:179161800-179176600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:179161800-179176800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:179161800-179177400	Weak transcription	Fetal Kidney	kidney
10	chr5:179161800-179188800	Weak transcription	NHDF-Ad	bronchial
11	chr5:179162000-179176600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:179162000-179176600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:179162000-179176600	Weak transcription	Osteobl	bone
14	chr5:179162000-179176800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:179162000-179181200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:179162000-179181400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr5:179162000-179181800	Weak transcription	NHLF	lung
18	chr5:179162000-179186000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:179162000-179186000	Weak transcription	HSMM	muscle
20	chr5:179162000-179186200	Weak transcription	HMEC	breast
21	chr5:179162000-179186600	Weak transcription	Hela-S3	cervix
22	chr5:179162000-179190400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:179162600-179189000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr5:179163000-179176600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:179163200-179176600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr5:179163200-179176800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:179163200-179181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:179163400-179175600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:179163400-179176600	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:179163800-179180000	Weak transcription	Fetal Brain Male	brain
31	chr5:179164400-179179000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:179164400-179181600	Weak transcription	HUVEC	blood vessel
33	chr5:179164600-179186600	Weak transcription	NH-A	brain
34	chr5:179165000-179176600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:179165000-179176600	Weak transcription	Adipose Nuclei	Adipose
36	chr5:179165000-179176600	Weak transcription	Brain Substantia Nigra	brain
37	chr5:179165000-179176600	Weak transcription	Pancreas	Pancrea
38	chr5:179165000-179181200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr5:179165400-179176600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:179165400-179176800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:179165400-179184600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:179165600-179176800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:179165600-179181800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr5:179165800-179176400	Weak transcription	K562	blood
45	chr5:179165800-179188800	Weak transcription	Brain Germinal Matrix	brain
46	chr5:179166000-179176600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr5:179166000-179176800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr5:179166200-179181200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr5:179166400-179181400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:179166400-179181400	Weak transcription	Fetal Intestine Large	intestine

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