Variant report

Variant	rs4859609
Chromosome Location	chr4:76999197-76999198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10002977	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10007919	0.95[CHB][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs10029157	0.80[EUR][1000 genomes]
rs10031983	0.95[CHB][hapmap];0.81[EUR][1000 genomes]
rs10518143	0.81[CHB][hapmap]
rs12374321	0.83[GIH][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs12649185	0.81[EUR][1000 genomes]
rs12651402	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13111494	0.95[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs13118503	0.87[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs13121161	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13130917	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs17001247	0.87[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs1857821	0.87[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs2242470	0.87[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs2271528	0.87[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs2276886	0.81[CHB][hapmap];0.94[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs28655366	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2869462	0.86[CHB][hapmap]
rs28818603	0.81[EUR][1000 genomes]
rs3733238	0.87[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs4429750	0.83[EUR][1000 genomes]
rs4859567	0.90[MEX][hapmap]
rs4859571	0.83[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs4859572	0.85[MEX][hapmap];0.82[TSI][hapmap]
rs4859578	0.87[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs6841333	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6847815	0.87[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs7688312	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs884004	0.86[CHB][hapmap];0.94[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs9307076	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs9994667	0.95[CHB][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4859609	NAAA	cis	Muscle Skeletal	GTEx
rs4859609	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs4859609	CXCL10	cis	lymphoblastoid	seeQTL
rs4859609	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs4859609	NAAA	cis	Esophagus Muscularis	GTEx
rs4859609	NAAA	cis	lymphoblastoid	seeQTL
rs4859609	NAAA	cis	Esophagus Mucosa	GTEx
rs4859609	FAM47E	cis	cerebellum	SCAN
rs4859609	CDKL2	cis	parietal	SCAN
rs4859609	NAAA	cis	parietal	SCAN
rs4859609	NAAA	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76995600-76999400	Active TSS	Psoas Muscle	Psoas
2	chr4:76995600-77000800	Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr4:76997000-77007200	Weak transcription	Fetal Brain Male	brain
4	chr4:76997000-77008000	Weak transcription	Brain Angular Gyrus	brain
5	chr4:76998400-77001000	Enhancers	Fetal Heart	heart
6	chr4:76998600-76999400	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr4:76998800-76999800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:76998800-77000000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr4:76999000-76999600	Enhancers	Liver	Liver
10	chr4:76999000-77008200	Weak transcription	Right Ventricle	heart

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