Variant report

Variant	rs4241577
Chromosome Location	chr4:76930776-76930777
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10007919	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10009947	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10021434	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10029157	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10031733	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10031983	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10518143	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12374321	0.83[AMR][1000 genomes]
rs12374370	0.82[AMR][1000 genomes]
rs12649185	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13112512	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13118503	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13129896	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17001247	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1857821	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2242470	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2271528	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2276886	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28375800	0.80[AMR][1000 genomes]
rs28422144	0.80[AMR][1000 genomes]
rs28451731	0.80[AMR][1000 genomes]
rs28532601	0.80[AMR][1000 genomes]
rs28535831	0.80[AMR][1000 genomes]
rs28588114	0.83[AMR][1000 genomes]
rs28595360	0.83[AMR][1000 genomes]
rs28647886	0.80[AMR][1000 genomes]
rs2869462	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34740469	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3733238	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3796484	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4429750	0.85[EUR][1000 genomes]
rs4859570	0.80[AMR][1000 genomes]
rs4859571	0.80[AMR][1000 genomes]
rs4859572	0.82[AMR][1000 genomes]
rs4859573	0.83[AMR][1000 genomes]
rs4859577	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859578	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4859580	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55876513	0.81[EUR][1000 genomes]
rs6847815	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs884004	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9994667	0.80[AMR][1000 genomes];0.86[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	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4241577	NAAA	cis	Esophagus Muscularis	GTEx
rs4241577	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs4241577	NAAA	cis	Muscle Skeletal	GTEx
rs4241577	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs4241577	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs4241577	NAAA	cis	Esophagus Mucosa	GTEx
rs4241577	NAAA	cis	Adipose Subcutaneous	GTEx
rs4241577	NAAA	cis	Whole Blood	GTEx
rs4241577	NAAA	cis	Artery Aorta	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76912400-76932200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:76928800-76932400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:76928800-76932400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:76928800-76932600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:76929000-76932400	Weak transcription	HMEC	breast
6	chr4:76929000-76932400	Weak transcription	NHEK	skin
7	chr4:76929000-76934200	Weak transcription	Fetal Intestine Small	intestine
8	chr4:76929200-76932600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:76929200-76932600	Weak transcription	Liver	Liver

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