Variant report

Variant	rs4890122
Chromosome Location	chr17:38876841-38876842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2109223	0.82[ASN][1000 genomes]
rs2159430	0.80[ASN][1000 genomes]
rs2253717	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2462962	0.84[ASN][1000 genomes]
rs2462963	0.84[ASN][1000 genomes]
rs2462964	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2462970	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2469818	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58630924	0.83[ASN][1000 genomes]
rs7212255	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs726848	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs758630	0.81[EUR][1000 genomes];0.87[ASN][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	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv908226	chr17:38876409-39003217	Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4890122	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs4890122	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs4890122	KRT24	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38860000-38890200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr17:38874400-38878600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr17:38875000-38879600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr17:38875800-38877200	Weak transcription	A549	lung
5	chr17:38876400-38877600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:38876400-38878600	Weak transcription	Hela-S3	cervix
7	chr17:38876600-38878200	Weak transcription	Placenta Amnion	Placenta Amnion

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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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