Variant report

Variant	rs13183239
Chromosome Location	chr5:108232464-108232465
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10515395	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11949314	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11949596	0.94[AMR][1000 genomes]
rs11955045	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13169856	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13171190	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13174393	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13174528	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13177718	0.94[AMR][1000 genomes]
rs13181901	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13183520	0.94[AMR][1000 genomes]
rs13185815	0.94[AMR][1000 genomes]
rs34188045	0.94[AMR][1000 genomes]
rs34349846	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34494089	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs34609891	0.94[AMR][1000 genomes]
rs34793372	0.94[AMR][1000 genomes]
rs35137434	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35238524	0.94[AMR][1000 genomes]
rs35290386	0.89[AMR][1000 genomes]
rs35316595	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35603379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35746105	0.94[AMR][1000 genomes]
rs35767331	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35778913	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35893408	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35940503	0.94[AMR][1000 genomes]
rs36047276	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36054201	0.89[AMR][1000 genomes]
rs55665982	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55960958	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71586586	0.89[AMR][1000 genomes]
rs71592766	0.94[AMR][1000 genomes]
rs71592767	0.94[AMR][1000 genomes]
rs71592769	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs71592772	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71592774	1.00[AMR][1000 genomes];0.98[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	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv471039	chr5:108133967-108245089	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1016343	chr5:108220116-108364687	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv882691	chr5:108229760-108366473	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108173400-108239800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:108183800-108260400	Weak transcription	Ovary	ovary
3	chr5:108194600-108260000	Weak transcription	Fetal Intestine Large	intestine
4	chr5:108194800-108236200	Weak transcription	Hela-S3	cervix
5	chr5:108195200-108234400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:108197000-108268200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr5:108198600-108235000	Weak transcription	Fetal Kidney	kidney
8	chr5:108199200-108271400	Weak transcription	Aorta	Aorta
9	chr5:108200200-108232600	Weak transcription	Brain Angular Gyrus	brain
10	chr5:108200200-108246400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:108203800-108323400	Weak transcription	Primary B cells from cord blood	blood
12	chr5:108204400-108237800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr5:108205400-108241400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:108208200-108268800	Weak transcription	Primary T cells from cord blood	blood
15	chr5:108209800-108234000	Weak transcription	HMEC	breast
16	chr5:108209800-108234400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:108212800-108236200	Weak transcription	NHDF-Ad	bronchial
18	chr5:108214200-108272200	Weak transcription	Gastric	stomach
19	chr5:108217200-108233600	Weak transcription	Esophagus	oesophagus
20	chr5:108217200-108236600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:108217400-108233200	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:108217400-108244200	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr5:108217400-108253200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:108217600-108323200	Weak transcription	Left Ventricle	heart
25	chr5:108221000-108236200	Weak transcription	NH-A	brain
26	chr5:108221000-108236400	Weak transcription	NHLF	lung
27	chr5:108221000-108241200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:108221200-108234400	Weak transcription	HUVEC	blood vessel
29	chr5:108221200-108236200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:108221200-108236200	Weak transcription	Osteobl	bone
31	chr5:108221400-108280600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:108221600-108238200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:108223400-108236800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:108223400-108247000	Weak transcription	Brain Substantia Nigra	brain
35	chr5:108223800-108233600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:108227000-108233400	Weak transcription	Fetal Lung	lung
37	chr5:108227400-108234400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:108227600-108244400	Weak transcription	Right Ventricle	heart
39	chr5:108227800-108245200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr5:108228200-108240200	Weak transcription	Fetal Heart	heart
41	chr5:108228600-108236000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr5:108228600-108247600	Weak transcription	Liver	Liver
43	chr5:108229600-108244200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr5:108229600-108269800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:108230200-108232800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:108230200-108234000	Weak transcription	NHEK	skin
47	chr5:108230200-108239800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:108230200-108302400	Weak transcription	HSMM	muscle
49	chr5:108230400-108232800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr5:108230400-108232800	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links