Variant report

Variant	rs11582424
Chromosome Location	chr1:154363985-154363986
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1073907	0.83[AMR][1000 genomes]
rs10908834	0.83[EUR][1000 genomes]
rs10908835	0.94[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11265593	0.81[AMR][1000 genomes]
rs11265606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265607	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265609	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576181	0.81[AMR][1000 genomes]
rs11576193	0.81[AMR][1000 genomes]
rs11577266	0.83[AMR][1000 genomes]
rs11580178	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11585004	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12127600	0.94[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs12719998	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12738097	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1889314	0.84[EUR][1000 genomes]
rs1889315	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34437053	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56211693	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61803410	0.81[AMR][1000 genomes]
rs6427627	0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6427631	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6657938	0.81[AMR][1000 genomes]
rs6659828	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6661909	0.83[EUR][1000 genomes]
rs6696089	0.81[AMR][1000 genomes]
rs6698130	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7525436	0.83[EUR][1000 genomes]
rs952146	0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9651054	0.86[ASN][1000 genomes]
rs9662562	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9724691	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9728585	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11582424	TARS2	cis	parietal	SCAN
rs11582424	SHC1	cis	parietal	SCAN
rs11582424	SLC39A1	cis	cerebellum	SCAN
rs11582424	GATAD2B	cis	parietal	SCAN
rs11582424	S100A5	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154358600-154364000	Weak transcription	Hela-S3	cervix
2	chr1:154359600-154364000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:154360400-154370000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:154360800-154364200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:154363200-154364400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:154363400-154364600	Enhancers	NHEK	skin
7	chr1:154363600-154364200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:154363600-154364400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:154363600-154364400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:154363600-154364400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:154363600-154364400	Enhancers	Esophagus	oesophagus
12	chr1:154363600-154364400	Enhancers	HMEC	breast
13	chr1:154363800-154364200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:154363800-154364400	Enhancers	Monocytes-CD14+_RO01746	blood

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