Variant report

Variant	rs4855835
Chromosome Location	chr3:49647821-49647822
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1060962	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11130212	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11919311	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12490267	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12497288	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1352890	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1873626	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2005557	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2131104	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2131109	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2329020	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2960548	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35007338	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35404120	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855847	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855852	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4855881	0.84[AMR][1000 genomes]
rs4855883	0.81[AMR][1000 genomes]
rs4855884	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6765869	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4855835	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4855835	IHPK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49637800-49653600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49641200-49653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:49644600-49648800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:49645400-49648200	Weak transcription	Esophagus	oesophagus
5	chr3:49645400-49648200	Weak transcription	Stomach Mucosa	stomach
6	chr3:49645800-49653600	Weak transcription	Fetal Lung	lung
7	chr3:49646600-49649200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:49646800-49648400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:49646800-49648600	Enhancers	Brain Hippocampus Middle	brain
10	chr3:49646800-49648600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:49646800-49648600	Enhancers	Brain Substantia Nigra	brain
12	chr3:49646800-49648600	Enhancers	Fetal Stomach	stomach
13	chr3:49646800-49648800	Enhancers	Brain Angular Gyrus	brain
14	chr3:49646800-49649000	Enhancers	Brain Anterior Caudate	brain
15	chr3:49646800-49649000	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:49646800-49649400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:49647000-49649400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:49647000-49649600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:49647200-49648200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:49647200-49648200	Weak transcription	NHDF-Ad	bronchial
21	chr3:49647200-49648400	Enhancers	Brain Germinal Matrix	brain
22	chr3:49647400-49648200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr3:49647400-49649000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:49647400-49653400	Weak transcription	Fetal Brain Female	brain
25	chr3:49647800-49653000	Weak transcription	Fetal Heart	heart

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