Variant report

Variant	rs3820039
Chromosome Location	chr1:86909703-86909704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10493790	0.86[ASW][hapmap];0.84[MEX][hapmap]
rs10873785	0.93[ASN][1000 genomes]
rs11161814	0.81[CHB][hapmap]
rs11161831	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12146009	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1413431	0.86[ASW][hapmap];0.84[MEX][hapmap]
rs17409304	0.86[ASW][hapmap];0.84[MEX][hapmap]
rs1814203	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs272493	0.82[JPT][hapmap]
rs272497	0.82[JPT][hapmap]
rs421105	0.84[MEX][hapmap]
rs57160573	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72720116	0.83[ASN][1000 genomes]
rs72720130	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7518184	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][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	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3820039	COL24A1	cis	parietal	SCAN
rs3820039	LOC339524	cis	cerebellum	SCAN
rs3820039	C1orf180	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86896600-86914400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:86897200-86922600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:86897200-86922800	Strong transcription	HMEC	breast
4	chr1:86897400-86916000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:86902000-86913200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:86903400-86926800	Weak transcription	Esophagus	oesophagus
7	chr1:86907600-86911600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:86908200-86911800	Weak transcription	Thymus	Thymus
9	chr1:86908800-86912400	Weak transcription	NHEK	skin
10	chr1:86909000-86911600	Weak transcription	Fetal Thymus	thymus
11	chr1:86909400-86910600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured 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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