Variant report

Variant	rs11158959
Chromosome Location	chr14:25370155-25370156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12432024	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12432042	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs16757	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3742523	0.84[CHD][hapmap];0.80[MEX][hapmap]
rs4983023	0.87[MEX][hapmap]
rs4983024	0.87[MEX][hapmap]
rs55903316	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56294606	0.81[EUR][1000 genomes]
rs7161445	0.81[EUR][1000 genomes]
rs725230	0.87[MEX][hapmap]
rs8019575	0.87[MEX][hapmap]
rs9743469	0.82[CHD][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	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
4	nsv901506	chr14:25295551-25377188	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1041445	chr14:25326692-25388290	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv901508	chr14:25365505-25451903	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11158959	NYNRIN	cis	cerebellum	SCAN
rs11158959	NYNRIN	cis	parietal	SCAN
rs11158959	OR10G2	cis	cerebellum	SCAN
rs11158959	SLC7A8	cis	cerebellum	SCAN
rs11158959	CHD8	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25362400-25378400	Weak transcription	Lung	lung
2	chr14:25364600-25372400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr14:25364800-25379800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr14:25366200-25377000	Weak transcription	Left Ventricle	heart
5	chr14:25366200-25377000	Weak transcription	Pancreas	Pancrea
6	chr14:25369000-25370800	Enhancers	NHDF-Ad	bronchial
7	chr14:25369200-25370200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr14:25369200-25370400	Enhancers	Adipose Nuclei	Adipose
9	chr14:25369200-25370400	Enhancers	Brain Angular Gyrus	brain
10	chr14:25369200-25370600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr14:25369400-25370200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr14:25369400-25370200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr14:25369400-25370200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr14:25369400-25370200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:25369400-25370200	Enhancers	Brain Cingulate Gyrus	brain
16	chr14:25369400-25370200	Enhancers	Brain Hippocampus Middle	brain
17	chr14:25369400-25370200	Enhancers	Fetal Heart	heart
18	chr14:25369400-25370200	Enhancers	Fetal Stomach	stomach
19	chr14:25369400-25370200	Enhancers	NHLF	lung
20	chr14:25369400-25370400	Enhancers	Brain Substantia Nigra	brain
21	chr14:25369600-25370200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr14:25369600-25370200	Enhancers	Colon Smooth Muscle	Colon
23	chr14:25369800-25370200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr14:25369800-25370200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr14:25369800-25370200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr14:25369800-25370400	Enhancers	Osteobl	bone
27	chr14:25369800-25370800	Enhancers	Brain Anterior Caudate	brain
28	chr14:25369800-25372400	Weak transcription	HSMMtube	muscle
29	chr14:25370000-25370200	Flanking Active TSS	Fetal Lung	lung
30	chr14:25370000-25370200	Enhancers	Right Atrium	heart
31	chr14:25370000-25370800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:25370000-25372000	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links