Variant report

Variant	rs4859580
Chromosome Location	chr4:76893680-76893681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10007919	0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[EUR][1000 genomes]
rs10009947	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10021434	0.80[CEU][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10029157	0.81[EUR][1000 genomes]
rs10031733	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031983	0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs10518143	0.80[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12374321	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12374370	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12649185	0.81[EUR][1000 genomes]
rs13111494	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs13112512	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118503	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13129896	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13130917	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs17001247	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1857821	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242470	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271528	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276886	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28375800	0.89[ASN][1000 genomes]
rs28422144	0.81[ASN][1000 genomes]
rs28451731	0.89[ASN][1000 genomes]
rs28532601	0.89[ASN][1000 genomes]
rs28535831	0.89[ASN][1000 genomes]
rs28588114	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28595360	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28647886	0.89[ASN][1000 genomes]
rs2869462	0.80[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34630680	0.91[ASN][1000 genomes]
rs34740469	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733238	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796484	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4241577	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4859567	0.94[CEU][hapmap]
rs4859570	0.89[ASN][1000 genomes]
rs4859571	0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4859572	0.83[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs4859573	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4859577	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859578	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55876513	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66498356	0.89[ASN][1000 genomes]
rs6847815	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs884004	0.83[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9994667	0.89[CEU][hapmap];0.81[CHB][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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4859580	NAAA	cis	Muscle Skeletal	GTEx
rs4859580	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs4859580	NAAA	cis	Esophagus Muscularis	GTEx
rs4859580	ASAHL	cis	multi-tissue	Pritchard
rs4859580	NAAA	cis	Artery Aorta	GTEx
rs4859580	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs4859580	NAAA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76862000-76896600	Weak transcription	Stomach Mucosa	stomach
2	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:76867800-76900000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
6	chr4:76868000-76899800	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:76868000-76903000	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:76868000-76903000	Strong transcription	Stomach Smooth Muscle	stomach
9	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
15	chr4:76869200-76900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:76870800-76897600	Strong transcription	Brain Germinal Matrix	brain
17	chr4:76872200-76902800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:76876800-76895200	Strong transcription	Fetal Kidney	kidney
19	chr4:76882400-76898200	Weak transcription	Aorta	Aorta
20	chr4:76883800-76899800	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr4:76883800-76903000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr4:76884000-76902800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:76884200-76899600	Strong transcription	Placenta Amnion	Placenta Amnion
24	chr4:76884200-76899800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:76884200-76902800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:76884200-76903800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr4:76884400-76897400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:76884600-76895600	Strong transcription	Fetal Brain Female	brain
29	chr4:76884600-76895800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:76884600-76896000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:76884600-76897400	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr4:76884600-76899800	Strong transcription	NH-A	brain
33	chr4:76884600-76899800	Strong transcription	Osteobl	bone
34	chr4:76884600-76902800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:76884600-76902800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:76884600-76902800	Strong transcription	Adipose Nuclei	Adipose
37	chr4:76884600-76903400	Strong transcription	HMEC	breast
38	chr4:76884600-76903400	Strong transcription	HSMM	muscle
39	chr4:76884600-76903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:76884600-76903600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:76884600-76903800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr4:76884800-76895400	Strong transcription	Brain Angular Gyrus	brain
43	chr4:76884800-76899400	Strong transcription	HUVEC	blood vessel
44	chr4:76884800-76899800	Strong transcription	HepG2	liver
45	chr4:76884800-76900000	Strong transcription	Brain Hippocampus Middle	brain
46	chr4:76884800-76900000	Strong transcription	Left Ventricle	heart
47	chr4:76884800-76900800	Strong transcription	K562	blood
48	chr4:76884800-76902200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:76884800-76902600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr4:76884800-76903600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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