Variant report

Variant	rs584397
Chromosome Location	chr18:43556952-43556953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10432160	0.94[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10432197	0.94[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11082498	0.80[ASN][1000 genomes]
rs1573404	0.81[ASN][1000 genomes]
rs2118618	0.89[AMR][1000 genomes]
rs3745000	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4629066	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs475452	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs481755	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57531499	0.82[ASN][1000 genomes]
rs60866799	0.81[ASN][1000 genomes]
rs61449207	0.84[ASN][1000 genomes]
rs630625	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6507652	0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs7226881	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7230104	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7235629	0.81[ASN][1000 genomes]
rs7238724	0.91[EUR][1000 genomes]
rs7242733	0.82[EUR][1000 genomes]
rs72918390	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8086401	0.81[ASN][1000 genomes]
rs8087546	0.81[ASN][1000 genomes]
rs8088153	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8093119	0.94[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8098175	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9955285	0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs9959763	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9963463	0.86[CHB][hapmap];0.84[CHD][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs9964220	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9964347	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2277	chr18:43543715-43588579	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv817792	chr18:43556952-43561238	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs584397	ATP5A1	cis	parietal	SCAN
rs584397	KIAA1632	cis	lymphoblastoid	seeQTL
rs584397	KIAA1632	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43548000-43567000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:43548200-43562800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr18:43554200-43567200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr18:43554400-43558200	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr18:43554400-43566200	Weak transcription	Liver	Liver
6	chr18:43554600-43557000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr18:43554600-43557200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr18:43554600-43557200	Weak transcription	HUVEC	blood vessel
9	chr18:43554600-43557400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr18:43554600-43558800	Weak transcription	Primary B cells from cord blood	blood
11	chr18:43554600-43560000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr18:43554600-43560000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr18:43554600-43560000	Weak transcription	Fetal Heart	heart
14	chr18:43554600-43560000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr18:43554600-43560000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr18:43554600-43562600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr18:43554600-43563000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr18:43554600-43566200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr18:43554600-43566800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr18:43554600-43567400	Weak transcription	Adipose Nuclei	Adipose
21	chr18:43554600-43567800	Weak transcription	Primary T cells from cord blood	blood
22	chr18:43554600-43567800	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr18:43554600-43568000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr18:43554600-43568800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr18:43554600-43571400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr18:43554800-43558200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr18:43555000-43562600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr18:43555800-43557400	Enhancers	K562	blood
29	chr18:43556200-43557200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr18:43556400-43557200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr18:43556600-43557400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr18:43556800-43557200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr18:43556800-43557200	Enhancers	NHLF	lung
34	chr18:43556800-43557200	Enhancers	Osteobl	bone

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