Variant report

Variant	rs1793958
Chromosome Location	chr12:48392433-48392434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11168350	0.83[JPT][hapmap]
rs12423250	0.83[JPT][hapmap]
rs1635527	0.85[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1859443	0.83[JPT][hapmap]
rs7134203	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7134878	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7135261	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs954326	0.83[JPT][hapmap];0.81[LWK][hapmap]
rs9651981	0.83[JPT][hapmap]
rs9804751	0.83[JPT][hapmap]

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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1793958	IRAK4	cis	parietal	SCAN
rs1793958	SENP1	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48386800-48392800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48390000-48395000	Weak transcription	Right Atrium	heart
6	chr12:48390400-48394600	Weak transcription	Left Ventricle	heart
7	chr12:48390400-48394600	Weak transcription	Right Ventricle	heart
8	chr12:48391200-48394600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:48391600-48392800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:48391600-48393000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
11	chr12:48391600-48393200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:48391600-48394600	Weak transcription	Placenta	Placenta
13	chr12:48391800-48392600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:48392000-48392800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
15	chr12:48392200-48392600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
16	chr12:48392200-48392800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:48392200-48392800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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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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