Variant report

Variant	rs2442359
Chromosome Location	chr13:39304814-39304815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1037254	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2197887	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496434	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2496437	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2496446	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2496448	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496449	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496451	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9532273	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548443	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9548444	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs990909	0.84[EUR][1000 genomes];0.84[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	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2442359	FREM2	cis	parietal	SCAN
rs2442359	ZNF628	trans	cerebellum	SCAN
rs2442359	FREM2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39294800-39325000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr13:39298200-39339600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr13:39301000-39305400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:39303200-39308000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr13:39304400-39305600	Weak transcription	Fetal Stomach	stomach
6	chr13:39304800-39310400	Weak transcription	Rectal Smooth Muscle	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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