Variant report

Variant	rs2972071
Chromosome Location	chr2:55300749-55300750
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11674808	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13011689	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920862	0.95[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs2920878	0.91[CHB][hapmap];0.96[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2920900	0.83[ASN][1000 genomes]
rs2968790	0.85[ASN][1000 genomes]
rs2968793	0.86[ASN][1000 genomes]
rs2968794	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968795	0.91[CHB][hapmap];0.96[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2968798	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2968822	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2968825	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2968827	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972070	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972072	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2972075	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][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	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2972071	RTN4	cis	Esophagus Muscularis	GTEx
rs2972071	RTN4	cis	Artery Tibial	GTEx
rs2972071	RTN4	cis	Whole Blood	GTEx
rs2972071	RTN4	cis	Artery Aorta	GTEx
rs2972071	RTN4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55299200-55318000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:55299800-55301200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:55299800-55301400	Enhancers	Osteobl	bone
4	chr2:55300400-55301000	Enhancers	Fetal Heart	heart
5	chr2:55300600-55300800	Enhancers	Colon Smooth Muscle	Colon
6	chr2:55300600-55301400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:55300600-55301400	Enhancers	Fetal Brain Male	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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