Variant report

Variant	rs1499672
Chromosome Location	chr1:56037629-56037630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10749701	0.86[EUR][1000 genomes]
rs12127175	0.85[CEU][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs1304160	0.85[EUR][1000 genomes]
rs1499664	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs1514136	0.81[CEU][hapmap]
rs17410154	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs4927257	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs6684790	0.81[CEU][hapmap]
rs904604	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs904606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1499672	PODN	cis	parietal	SCAN
rs1499672	BSND	cis	parietal	SCAN
rs1499672	C1orf168	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56025800-56038400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:56035400-56043200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:56035800-56038000	Weak transcription	NHDF-Ad	bronchial
4	chr1:56035800-56038400	Weak transcription	NHLF	lung
5	chr1:56035800-56038600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:56036400-56039400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:56036400-56039400	Enhancers	Osteobl	bone
8	chr1:56036400-56041000	Weak transcription	Fetal Lung	lung
9	chr1:56037200-56038600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:56037200-56039800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr1:56037200-56047200	Weak transcription	Esophagus	oesophagus

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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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