Variant report

Variant	rs10146559
Chromosome Location	chr14:25579277-25579278
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12147239	0.86[JPT][hapmap]
rs12432850	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1571465	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17257773	0.86[JPT][hapmap]
rs1952503	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1958390	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1958391	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2031936	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031938	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2031939	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4644786	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61979909	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61979910	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8006005	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8019648	0.82[AFR][1000 genomes]
rs8020810	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs928075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv901509	chr14:25398571-25743484	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv901511	chr14:25505085-25588029	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3490801	chr14:25560793-25675699	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv3490802	chr14:25560793-25675699	Bivalent Enhancer Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10146559	NRL	cis	parietal	SCAN
rs10146559	DHRS1	cis	parietal	SCAN
rs10146559	PRMT5	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25577600-25579800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:25577600-25580000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr14:25577600-25580000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr14:25577600-25580200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr14:25577600-25581200	Enhancers	Fetal Heart	heart
6	chr14:25577800-25579600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr14:25577800-25579600	Enhancers	Brain Anterior Caudate	brain
8	chr14:25577800-25580200	Enhancers	HSMM	muscle
9	chr14:25577800-25580400	Enhancers	HSMMtube	muscle
10	chr14:25577800-25580800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr14:25577800-25580800	Enhancers	Brain Hippocampus Middle	brain
12	chr14:25577800-25581200	Enhancers	NHLF	lung
13	chr14:25577800-25582600	Enhancers	Placenta Amnion	Placenta Amnion
14	chr14:25578000-25579400	Enhancers	Fetal Intestine Small	intestine
15	chr14:25578000-25580200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr14:25578000-25580400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr14:25578000-25580600	Enhancers	Osteobl	bone
18	chr14:25578000-25580800	Enhancers	Brain Substantia Nigra	brain
19	chr14:25578000-25581200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr14:25578200-25579600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr14:25578200-25580600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr14:25578400-25579400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr14:25578400-25579600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr14:25578400-25579600	Weak transcription	Brain Angular Gyrus	brain
25	chr14:25578400-25580200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr14:25578400-25580600	Weak transcription	Right Atrium	heart
27	chr14:25578400-25580800	Enhancers	Brain Cingulate Gyrus	brain
28	chr14:25578400-25583400	Weak transcription	Psoas Muscle	Psoas
29	chr14:25578600-25580200	Weak transcription	Pancreas	Pancrea
30	chr14:25578600-25580600	Weak transcription	Left Ventricle	heart
31	chr14:25578600-25580600	Weak transcription	Right Ventricle	heart
32	chr14:25578600-25580600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr14:25578600-25582000	Weak transcription	Stomach Mucosa	stomach
34	chr14:25578600-25583600	Weak transcription	Gastric	stomach
35	chr14:25578800-25580400	Weak transcription	Fetal Lung	lung
36	chr14:25579200-25579400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr14:25579200-25579400	Enhancers	Colon Smooth Muscle	Colon
38	chr14:25579200-25579400	Flanking Active TSS	NHDF-Ad	bronchial
39	chr14:25579200-25580200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr14:25579200-25580200	Weak transcription	Fetal Intestine Large	intestine
41	chr14:25579200-25580400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr14:25579200-25580400	Enhancers	NH-A	brain
43	chr14:25579200-25580800	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr14:25579200-25581200	Enhancers	Fetal Muscle Leg	muscle

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