Variant report

Variant	rs13412839
Chromosome Location	chr2:54987215-54987216
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10201670	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13390196	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13396649	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13401661	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13422751	0.85[ASN][1000 genomes]
rs17046283	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17046292	0.96[ASN][1000 genomes]
rs2033414	0.86[ASN][1000 genomes]
rs2033415	0.86[ASN][1000 genomes]
rs4671974	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671976	0.85[ASN][1000 genomes]
rs59516754	0.86[ASN][1000 genomes]
rs62136877	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6712305	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7565441	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868700	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9711112	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv1844855	chr2:54987215-55012202	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13412839	ERLEC1	cis	cerebellum	SCAN
rs13412839	CCDC85A	cis	cerebellum	SCAN
rs13412839	SPTBN1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54983600-54991600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:54984800-54991000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:54985200-54990800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:54985600-54988600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:54985800-54995400	Weak transcription	Primary B cells from cord blood	blood
6	chr2:54986200-54987400	Weak transcription	GM12878-XiMat	blood
7	chr2:54986400-54987600	Weak transcription	NHDF-Ad	bronchial
8	chr2:54986400-54991000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:54986400-54991600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:54986800-54991200	Weak transcription	NHEK	skin

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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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