Variant report

Variant	rs3796058
Chromosome Location	chr2:172942448-172942449
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10167594	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs10171214	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs10209911	0.86[ASN][1000 genomes]
rs1038564	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10497377	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs10930503	0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11892858	0.86[JPT][hapmap]
rs12052482	0.86[ASN][1000 genomes]
rs12328877	0.83[ASN][1000 genomes]
rs12616766	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs12622144	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs13403822	0.91[JPT][hapmap]
rs1344393	0.86[ASN][1000 genomes]
rs17428076	0.92[MEX][hapmap]
rs17428174	0.85[MEX][hapmap]
rs17500114	1.00[MEX][hapmap]
rs17581610	0.86[JPT][hapmap]
rs17615589	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs17615607	0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2357323	0.86[ASN][1000 genomes]
rs56923699	0.85[ASN][1000 genomes]
rs57656367	0.86[ASN][1000 genomes]
rs62183811	0.81[AMR][1000 genomes]
rs62183817	0.83[AMR][1000 genomes]
rs62183851	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62183853	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6751078	0.86[JPT][hapmap]
rs73976544	0.86[ASN][1000 genomes]
rs73976547	0.86[ASN][1000 genomes]
rs788164	0.90[JPT][hapmap]
rs788168	0.92[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv875412	chr2:172903124-172942448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3796058	SLC25A12	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172911200-172947200	Weak transcription	HSMM	muscle
2	chr2:172917800-172944800	Weak transcription	Brain Substantia Nigra	brain
3	chr2:172931600-172944800	Weak transcription	Ovary	ovary
4	chr2:172931800-172942600	Weak transcription	K562	blood
5	chr2:172934000-172943200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:172940600-172942800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:172940800-172944000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:172941200-172943400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:172942000-172947000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:172942400-172944400	Flanking Active TSS	Brain Germinal Matrix	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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