Variant report

Variant	rs16862928
Chromosome Location	chr3:150591754-150591755
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10513379	0.82[CEU][hapmap]
rs1220544	0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs12629256	0.84[EUR][1000 genomes]
rs1444198	0.93[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes]
rs1444199	0.95[EUR][1000 genomes]
rs16862877	0.93[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs17283761	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs2034158	0.95[EUR][1000 genomes]
rs2037408	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs2037409	0.93[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs4680007	0.81[CHB][hapmap]
rs56659353	0.93[EUR][1000 genomes]
rs60107900	0.96[EUR][1000 genomes]
rs61132047	0.82[EUR][1000 genomes]
rs67193230	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73152585	0.95[EUR][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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv877646	chr3:150582992-150641304	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16862928	TM4SF4	cis	parietal	SCAN
rs16862928	UBQLN4	cis	parietal	SCAN
rs16862928	FAM194A	cis	parietal	SCAN
rs16862928	TM4SF4	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150586400-150597000	Weak transcription	Left Ventricle	heart
2	chr3:150589000-150592400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:150589000-150592600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:150589200-150592400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:150589400-150592400	Weak transcription	HSMMtube	muscle
6	chr3:150589800-150593200	Weak transcription	Fetal Heart	heart
7	chr3:150590600-150592200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:150591200-150595000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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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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