Variant report

Variant	rs9548380
Chromosome Location	chr13:39094288-39094289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10507473	0.87[EUR][1000 genomes]
rs12875233	0.94[JPT][hapmap]
rs2323932	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34903169	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9315594	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9315595	0.94[JPT][hapmap]
rs9532246	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9532249	0.84[EUR][1000 genomes]
rs9548376	0.84[EUR][1000 genomes]
rs9548377	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9548379	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548381	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548382	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548412	0.94[JPT][hapmap]
rs9566343	0.80[ASN][1000 genomes]
rs9576557	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576558	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9635094	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9548380	SOHLH2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39088400-39101200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:39092400-39095000	Enhancers	H1 Cell Line	embryonic stem cell
3	chr13:39092800-39094400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:39093200-39102400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr13:39093400-39094800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr13:39093800-39094400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
7	chr13:39093800-39094600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr13:39093800-39097400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:39094000-39094600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr13:39094000-39095200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr13:39094200-39094600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr13:39094200-39094800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr13:39094200-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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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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