Variant report

Variant	rs13096549
Chromosome Location	chr3:159742913-159742914
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10433458	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13065738	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2279741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679868	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66785795	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824967	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9852519	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9877910	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9881959	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829769	chr3:159606913-159805282	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv1806743	chr3:159723529-159744022	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13096549	IFT80	cis	parietal	SCAN
rs13096549	SCHIP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159741200-159744000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:159741400-159743000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:159741600-159744600	Weak transcription	NH-A	brain
4	chr3:159741600-159744600	Weak transcription	NHLF	lung
5	chr3:159741600-159744800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:159741600-159745200	Weak transcription	HMEC	breast
7	chr3:159741800-159743600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:159742000-159743000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:159742200-159744400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:159742200-159744400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:159742200-159744600	Weak transcription	NHDF-Ad	bronchial
12	chr3:159742400-159743800	Weak transcription	iPS DF 19.11 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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