Variant report

Variant	rs58662524
Chromosome Location	chr13:40112259-40112260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10459367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12585456	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17060245	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58418761	0.87[EUR][1000 genomes]
rs58918104	0.87[EUR][1000 genomes]
rs59531868	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72621301	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72621302	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72623303	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs72623305	0.87[EUR][1000 genomes]
rs9315708	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9566452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9566455	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576844	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576845	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576846	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576847	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576849	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576853	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576855	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576856	0.95[EUR][1000 genomes]
rs9576857	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9576858	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9576860	0.93[EUR][1000 genomes]
rs9576863	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9576864	0.87[EUR][1000 genomes]
rs9576867	0.87[EUR][1000 genomes]
rs9576868	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1050137	chr13:40090742-40118499	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40106000-40113200	Weak transcription	Fetal Lung	lung
2	chr13:40106200-40113200	Weak transcription	Colon Smooth Muscle	Colon
3	chr13:40106400-40113400	Weak transcription	HSMM	muscle
4	chr13:40106400-40113600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr13:40106400-40116600	Weak transcription	Fetal Muscle Leg	muscle
6	chr13:40106600-40113400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr13:40106600-40117400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:40106800-40124000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr13:40107800-40140200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr13:40108400-40113200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr13:40109000-40112600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr13:40109000-40113600	Weak transcription	Fetal Brain Female	brain
13	chr13:40109000-40114000	Enhancers	NHDF-Ad	bronchial
14	chr13:40109600-40113000	Weak transcription	Osteobl	bone
15	chr13:40110800-40113200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:40110800-40113600	Weak transcription	Esophagus	oesophagus
17	chr13:40110800-40115200	Weak transcription	Right Atrium	heart
18	chr13:40111200-40113000	Enhancers	Fetal Brain Male	brain
19	chr13:40111200-40133200	Weak transcription	Aorta	Aorta
20	chr13:40111400-40113400	Weak transcription	Ovary	ovary
21	chr13:40111400-40113600	Weak transcription	Adipose Nuclei	Adipose
22	chr13:40111400-40115200	Weak transcription	Left Ventricle	heart
23	chr13:40111400-40115200	Weak transcription	Right Ventricle	heart
24	chr13:40111400-40128200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:40111600-40112600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr13:40111600-40113400	Weak transcription	Psoas Muscle	Psoas
27	chr13:40111600-40113400	Weak transcription	NHLF	lung
28	chr13:40111600-40120600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr13:40111600-40128600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr13:40111800-40113000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr13:40111800-40117400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr13:40112000-40113000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:40112000-40117600	Weak transcription	NHEK	skin
34	chr13:40112000-40122400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:40112200-40112600	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links