Variant report

Variant	rs9548183
Chromosome Location	chr13:38661893-38661894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1924179	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1924192	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3967019	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4941885	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4943563	0.84[AMR][1000 genomes]
rs6563582	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7992222	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9532173	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9548182	0.85[ASN][1000 genomes]
rs9548185	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548186	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548188	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9548189	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9548193	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576448	0.80[EUR][1000 genomes]
rs9603319	0.82[AMR][1000 genomes]
rs9603322	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949406	chr13:38561474-39033484	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv900000	chr13:38608928-38710260	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv900001	chr13:38619750-38710260	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv900002	chr13:38628041-38710260	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3400710	chr13:38639001-38670017	Weak transcription ZNF genes & repeats Strong transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv518259	chr13:38648788-38661893	Weak transcription ZNF genes & repeats Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv900003	chr13:38648788-38710260	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv561511	chr13:38655046-38701046	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9548183	FREM2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38660200-38663000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
2	chr13:38661600-38662600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:38661600-38665200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:38661800-38664400	Weak transcription	Liver	Liver
5	chr13:38661800-38665000	Weak transcription	Pancreas	Pancrea
6	chr13:38661800-38669000	Weak transcription	Left Ventricle	heart

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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