Variant report

Variant	rs998549
Chromosome Location	chr15:73127139-73127140
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12594060	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12594938	0.83[MEX][hapmap]
rs1284048	0.84[ASN][1000 genomes]
rs12914505	0.85[ASN][1000 genomes]
rs1593508	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1974970	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053854	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2167031	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs2415168	0.85[ASN][1000 genomes]
rs4514651	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56058910	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62017630	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	nsv482512	chr15:73023099-73175952	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs998549	IQCH	cis	cerebellum	SCAN
rs998549	NR2E3	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73114400-73127200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr15:73118000-73129200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:73125000-73128400	Enhancers	Fetal Intestine Small	intestine
4	chr15:73125000-73128600	Enhancers	Fetal Intestine Large	intestine
5	chr15:73125400-73130600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr15:73126000-73132800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr15:73126400-73127400	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr15:73126400-73132000	Enhancers	Fetal Muscle Leg	muscle
9	chr15:73126800-73128200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr15:73127000-73127400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr15:73127000-73130800	Weak transcription	Ovary	ovary

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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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