Variant report

Variant	rs2413001
Chromosome Location	chr22:31249333-31249334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12160476	0.82[ASN][1000 genomes]
rs136223	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs136224	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2107401	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4820028	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4820907	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5753339	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8139392	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv588888	chr22:31212641-31249333	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv522377	chr22:31232074-31249333	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv914973	chr22:31232074-31264281	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv520242	chr22:31245745-31249333	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv524629	chr22:31245745-31254954	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv914974	chr22:31249333-31279536	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2413001	ZMAT5	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31238600-31251200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr22:31245600-31250800	Weak transcription	Hela-S3	cervix
3	chr22:31249000-31249400	ZNF genes & repeats	HSMM	muscle
4	chr22:31249000-31249400	ZNF genes & repeats	NHEK	skin
5	chr22:31249000-31250800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr22:31249200-31256400	Weak transcription	Brain Inferior Temporal Lobe	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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