Variant report

Variant	rs2590781
Chromosome Location	chr4:54523877-54523878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1079230	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477875	0.89[ASN][1000 genomes]
rs1477876	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1546526	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972815	0.89[CEU][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1996005	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164266	0.91[ASN][1000 genomes]
rs2572283	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2572291	0.89[ASN][1000 genomes]
rs2572299	0.89[ASN][1000 genomes]
rs2590780	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2590816	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2590823	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2616386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2616410	0.81[EUR][1000 genomes]
rs2668516	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2668521	0.89[ASN][1000 genomes]
rs2668524	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668529	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668548	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2668549	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668557	0.87[EUR][1000 genomes]
rs2668566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686480	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907510	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	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2590781	TXNDC9	cis	parietal	SCAN
rs2590781		cis	Lymphoblastoid	GTEx
rs2590781	FIP1L1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54520200-54524400	Weak transcription	Ovary	ovary
2	chr4:54520800-54524000	Weak transcription	Fetal Heart	heart
3	chr4:54521000-54524200	Weak transcription	Fetal Stomach	stomach
4	chr4:54522000-54524600	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:54522200-54526000	Weak transcription	Gastric	stomach
6	chr4:54522200-54526000	Weak transcription	Right Atrium	heart
7	chr4:54522400-54525400	Weak transcription	Stomach Mucosa	stomach
8	chr4:54523400-54524600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:54523400-54525400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:54523800-54524000	Enhancers	Placenta	Placenta
11	chr4:54523800-54524200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr4:54523800-54524200	Weak transcription	NHDF-Ad	bronchial

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