Variant report

Variant	rs2072038
Chromosome Location	chr1:175105778-175105779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1012466	0.94[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs1012467	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2072036	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2072039	0.93[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];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	nsv825487	chr1:175031609-175113572	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv508648	chr1:175056387-175121913	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2072038	TNFSF4	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175100000-175105800	Weak transcription	Adipose Nuclei	Adipose
2	chr1:175102000-175107600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:175105200-175105800	Enhancers	Fetal Stomach	stomach
4	chr1:175105200-175106200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:175105200-175110000	Weak transcription	GM12878-XiMat	blood
6	chr1:175105400-175106800	Enhancers	Liver	Liver
7	chr1:175105400-175107000	Weak transcription	Stomach Smooth Muscle	stomach

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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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