Variant report

Variant	rs2668524
Chromosome Location	chr4:54505850-54505851
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1079230	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107027	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477875	0.89[ASN][1000 genomes]
rs1477876	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1546526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972815	0.89[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1996005	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164266	0.91[ASN][1000 genomes]
rs2572283	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2572291	0.89[ASN][1000 genomes]
rs2572299	0.89[ASN][1000 genomes]
rs2590780	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2590781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590816	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2590823	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2616386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668516	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2668521	0.89[ASN][1000 genomes]
rs2668529	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668548	0.86[EUR][1000 genomes]
rs2668549	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668557	0.85[EUR][1000 genomes]
rs2668566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686480	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2668524	FIP1L1	cis	cerebellum	SCAN
rs2668524		cis	Lymphoblastoid	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54494600-54507000	Weak transcription	Right Ventricle	heart
2	chr4:54501400-54506400	Weak transcription	Stomach Mucosa	stomach
3	chr4:54501400-54507000	Weak transcription	Left Ventricle	heart
4	chr4:54501400-54507000	Weak transcription	Lung	lung
5	chr4:54501400-54510800	Weak transcription	Right Atrium	heart
6	chr4:54501600-54507000	Weak transcription	Fetal Intestine Large	intestine
7	chr4:54502200-54506600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:54502200-54507000	Weak transcription	Gastric	stomach
9	chr4:54502800-54506200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr4:54502800-54507000	Weak transcription	Pancreas	Pancrea
11	chr4:54502800-54507600	Weak transcription	Adipose Nuclei	Adipose
12	chr4:54503000-54506400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr4:54503000-54506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:54505600-54507600	Enhancers	GM12878-XiMat	blood
15	chr4:54505600-54508400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:54505800-54507400	Enhancers	Esophagus	oesophagus
17	chr4:54505800-54508000	Enhancers	Fetal Heart	heart

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