Variant report

Variant	rs1539348
Chromosome Location	chr6:73710903-73710904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10943073	0.87[GIH][hapmap]
rs10943076	0.84[CHD][hapmap];0.84[JPT][hapmap]
rs2000203	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2350748	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9341391	0.90[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][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	nsv830691	chr6:73530978-73743648	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1539348	CD109	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73607600-73715400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:73696800-73716400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:73705600-73717400	Weak transcription	Aorta	Aorta
4	chr6:73707000-73714600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:73709400-73711000	Enhancers	Brain Hippocampus Middle	brain
6	chr6:73709400-73711200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:73709600-73711000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:73709600-73711000	Enhancers	Brain Cingulate Gyrus	brain
9	chr6:73710000-73740000	Weak transcription	HMEC	breast
10	chr6:73710600-73717400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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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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