Variant report

Variant	rs17474808
Chromosome Location	chr2:39794046-39794047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11680972	0.84[EUR][1000 genomes]
rs12470310	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12994521	0.89[ASN][1000 genomes]
rs13015976	0.89[ASN][1000 genomes]
rs13020343	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13035388	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1405085	0.84[ASN][1000 genomes]
rs28812028	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4670944	0.84[ASN][1000 genomes]
rs4992380	0.87[AMR][1000 genomes]
rs6706561	0.87[EUR][1000 genomes]
rs6740771	0.90[EUR][1000 genomes]
rs71439259	0.84[ASN][1000 genomes]
rs7586289	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17474808	DHX57	cis	parietal	SCAN
rs17474808	MAP4K3	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39778800-39797400	Weak transcription	Fetal Heart	heart
2	chr2:39790200-39795000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:39791600-39794600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:39791600-39796000	Weak transcription	Right Atrium	heart
5	chr2:39792000-39794600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:39792000-39796800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:39792200-39794600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:39792200-39794600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:39792200-39798600	Weak transcription	Gastric	stomach
10	chr2:39792400-39795000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:39792600-39799400	Enhancers	Fetal Stomach	stomach
12	chr2:39793000-39796400	Enhancers	Fetal Muscle Leg	muscle
13	chr2:39793000-39796400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr2:39793200-39794400	Weak transcription	Aorta	Aorta
15	chr2:39793600-39794200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:39793600-39796800	Enhancers	Stomach Smooth Muscle	stomach
17	chr2:39793800-39794800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:39793800-39794800	Weak transcription	Fetal Lung	lung
19	chr2:39794000-39795400	Weak transcription	HepG2	liver

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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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