Variant report

Variant	rs3825413
Chromosome Location	chr13:86369120-86369121
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1054544	0.90[JPT][hapmap]
rs1337266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2210958	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2786177	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs437453	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs588790	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs593534	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs629601	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs647409	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs656142	0.86[EUR][1000 genomes]
rs659223	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs667264	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs682259	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs688445	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7322136	0.85[EUR][1000 genomes]
rs9319179	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9594052	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9594053	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][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	nsv1037563	chr13:85830511-86414012	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3825413	PRDX4	trans	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:86335000-86372800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:86362400-86371000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr13:86366400-86370600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:86366600-86369200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr13:86366600-86369600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:86366800-86370200	Weak transcription	Fetal Intestine Large	intestine
7	chr13:86367000-86372200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr13:86367200-86370800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr13:86367200-86371200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:86368200-86370000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:86368400-86369200	Genic enhancers	Fetal Lung	lung
12	chr13:86368600-86369200	Genic enhancers	Fetal Stomach	stomach
13	chr13:86368600-86369400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr13:86368800-86371400	Weak transcription	Rectal Mucosa Donor 31	rectum

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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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