Variant report

Variant	rs4992380
Chromosome Location	chr2:39810943-39810944
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12470310	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13031765	0.87[EUR][1000 genomes]
rs17474808	0.87[AMR][1000 genomes]
rs28812028	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6544235	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6722571	0.93[EUR][1000 genomes]
rs7597939	0.88[EUR][1000 genomes]
rs7605812	0.83[EUR][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	nsv833858	chr2:39684483-39856498	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv961312	chr2:39810592-39817719	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4992380	MAP4K3	cis	cerebellum	SCAN
rs4992380	CDC42EP3	cis	parietal	SCAN
rs4992380	DHX57	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39799400-39811600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:39799600-39820800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:39808400-39815200	Weak transcription	HepG2	liver
4	chr2:39808400-39819000	Weak transcription	Liver	Liver
5	chr2:39809400-39821000	Weak transcription	Psoas Muscle	Psoas
6	chr2:39810200-39812000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:39810200-39812400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:39810600-39812800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:39810800-39811800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:39810800-39812000	Enhancers	Fetal Kidney	kidney
11	chr2:39810800-39812200	Enhancers	HSMMtube	muscle
12	chr2:39810800-39812400	Enhancers	HSMM	muscle
13	chr2:39810800-39812600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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