Variant report

Variant	rs1455872
Chromosome Location	chr3:160416966-160416967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10433459	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11707740	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12638557	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13062999	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13092981	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1378659	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1378661	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16831361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17217147	0.87[EUR][1000 genomes]
rs2366967	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34275580	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35355599	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6791128	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7651855	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.98[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs7651941	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs959826	0.90[AMR][1000 genomes];0.81[EUR][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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1455872	IFT80	cis	parietal	SCAN
rs1455872	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160413600-160417200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:160414200-160417000	Enhancers	NH-A	brain
3	chr3:160415400-160417000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:160415400-160417000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr3:160415400-160417000	Enhancers	HUVEC	blood vessel
6	chr3:160415600-160417000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:160415600-160417200	Enhancers	Stomach Mucosa	stomach
8	chr3:160416600-160417000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr3:160416600-160419400	Weak transcription	NHLF	lung
10	chr3:160416600-160421800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:160416800-160417000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:160416800-160418800	Enhancers	Hela-S3	cervix
13	chr3:160416800-160421600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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