Variant report

Variant	rs16829231
Chromosome Location	chr2:134531622-134531623
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:134529817..134532379-chr2:134535821..134537604,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11674105	0.81[EUR][1000 genomes]
rs11681656	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13421881	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1374404	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1596914	0.81[EUR][1000 genomes]
rs1596915	0.80[EUR][1000 genomes]
rs16829379	0.81[EUR][1000 genomes]
rs2121412	0.81[EUR][1000 genomes]
rs2166540	0.81[EUR][1000 genomes]
rs3887003	0.81[EUR][1000 genomes]
rs4533516	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57520550	0.80[EUR][1000 genomes]
rs6712538	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73005736	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73007604	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73007615	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73007674	0.81[EUR][1000 genomes]
rs73007675	0.80[EUR][1000 genomes]
rs73007677	0.81[EUR][1000 genomes]
rs73007678	0.81[EUR][1000 genomes]
rs733170	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16829231	LOC440905	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134523600-134532400	Weak transcription	Right Ventricle	heart
2	chr2:134524600-134537200	Weak transcription	NHLF	lung
3	chr2:134524800-134531800	Weak transcription	Ovary	ovary
4	chr2:134527000-134532000	Weak transcription	Esophagus	oesophagus
5	chr2:134527000-134532000	Weak transcription	Right Atrium	heart
6	chr2:134530600-134533000	Enhancers	Fetal Lung	lung
7	chr2:134530800-134531800	Enhancers	Brain Hippocampus Middle	brain
8	chr2:134530800-134533200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:134531000-134532200	Enhancers	Brain Anterior Caudate	brain
10	chr2:134531000-134532800	Enhancers	Colon Smooth Muscle	Colon
11	chr2:134531000-134533000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:134531000-134533200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr2:134531200-134532400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr2:134531200-134532800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:134531200-134532800	Enhancers	Brain Cingulate Gyrus	brain
16	chr2:134531200-134532800	Enhancers	Fetal Heart	heart
17	chr2:134531200-134533000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:134531200-134533000	Enhancers	Brain Angular Gyrus	brain
19	chr2:134531200-134533000	Enhancers	Brain Substantia Nigra	brain
20	chr2:134531400-134532200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:134531400-134532800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:134531400-134532800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:134531400-134533000	Enhancers	Adipose Nuclei	Adipose
24	chr2:134531400-134533000	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr2:134531400-134533000	Enhancers	Fetal Brain Male	brain
26	chr2:134531400-134533000	Enhancers	Rectal Smooth Muscle	rectum
27	chr2:134531600-134532000	Enhancers	Stomach Smooth Muscle	stomach
28	chr2:134531600-134532400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:134531600-134532600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:134531600-134532800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:134531600-134532800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:134531600-134532800	Enhancers	Fetal Stomach	stomach
33	chr2:134531600-134532800	Enhancers	Left Ventricle	heart
34	chr2:134531600-134533000	Enhancers	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links