Variant report

Variant	rs55871867
Chromosome Location	chr1:210051029-210051030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1319435	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1415543	0.86[AMR][1000 genomes]
rs17015309	0.86[AMR][1000 genomes]
rs170554	0.83[AFR][1000 genomes]
rs17389436	0.83[AFR][1000 genomes]
rs2205984	0.86[AMR][1000 genomes]
rs2206043	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs227212	0.83[AFR][1000 genomes]
rs227213	0.83[AFR][1000 genomes]
rs227220	0.83[AFR][1000 genomes]
rs227222	0.83[AFR][1000 genomes]
rs57315825	0.88[ASN][1000 genomes]
rs59435160	0.88[ASN][1000 genomes]
rs60326345	0.88[ASN][1000 genomes]
rs61747285	0.86[AMR][1000 genomes]
rs735693	0.85[ASN][1000 genomes]
rs735694	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7540237	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7551944	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9430025	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55871867	TRAF3IP3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210041000-210055400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:210045200-210051400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:210047400-210051200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:210047400-210051200	Enhancers	HMEC	breast
5	chr1:210047400-210052600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:210047400-210053400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:210048800-210051800	Enhancers	Hela-S3	cervix
8	chr1:210049000-210051200	Enhancers	NHDF-Ad	bronchial
9	chr1:210049400-210052400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:210049400-210052400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:210049400-210052800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:210049400-210052800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:210049400-210056600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:210049800-210052200	Weak transcription	Brain Anterior Caudate	brain
15	chr1:210049800-210052200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:210049800-210052200	Weak transcription	Brain Substantia Nigra	brain
17	chr1:210049800-210052600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:210049800-210052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:210050000-210051200	Enhancers	NHEK	skin
20	chr1:210050000-210052400	Weak transcription	Brain Angular Gyrus	brain
21	chr1:210050000-210052800	Weak transcription	Osteobl	bone
22	chr1:210050200-210051200	Enhancers	HUVEC	blood vessel
23	chr1:210050200-210052400	Weak transcription	NH-A	brain
24	chr1:210050200-210052600	Weak transcription	HSMM	muscle
25	chr1:210050200-210052800	Weak transcription	Fetal Brain Female	brain
26	chr1:210050400-210052800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:210050600-210052200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:210050600-210052400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:210050600-210052600	Weak transcription	Brain Germinal Matrix	brain
30	chr1:210050800-210052400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:210050800-210052800	Weak transcription	HSMMtube	muscle
32	chr1:210051000-210052000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:210051000-210052000	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:210051000-210052600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:210051000-210057400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links