Variant report

Variant	rs6550259
Chromosome Location	chr3:34255372-34255373
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12054108	0.99[ASN][1000 genomes]
rs36094245	0.80[ASN][1000 genomes]
rs56032332	0.93[ASN][1000 genomes]
rs56106035	0.91[ASN][1000 genomes]
rs56302682	0.94[ASN][1000 genomes]
rs6780603	0.96[ASN][1000 genomes]
rs6784859	0.96[ASN][1000 genomes]
rs6808824	0.96[ASN][1000 genomes]
rs9311048	0.99[ASN][1000 genomes]
rs9985312	0.89[ASN][1000 genomes]
rs9985381	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001599	chr3:34149575-34437701	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv536533	chr3:34149575-34437701	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv876682	chr3:34149814-34401451	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv916961	chr3:34203879-34506554	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6550259	DLEC1	cis	parietal	SCAN
rs6550259	SUSD5	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:34252600-34255400	Enhancers	HUVEC	blood vessel
2	chr3:34253400-34255400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:34253400-34257200	Enhancers	Fetal Intestine Small	intestine
4	chr3:34253600-34255400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:34253600-34255600	Enhancers	Fetal Intestine Large	intestine
6	chr3:34254000-34257800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:34254000-34258400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:34254200-34257800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:34254400-34255600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:34255000-34255400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:34255000-34255400	Enhancers	Aorta	Aorta
12	chr3:34255000-34255400	Enhancers	Brain Angular Gyrus	brain
13	chr3:34255000-34255400	Enhancers	Left Ventricle	heart
14	chr3:34255200-34255400	Enhancers	Stomach Mucosa	stomach
15	chr3:34255200-34257800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:34255200-34259800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:34255200-34259800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:34255200-34261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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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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