Variant report

Variant	rs12494396
Chromosome Location	chr3:48178293-48178294
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48177580..48180354-chr3:48185664..48188328,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11130157	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11711766	0.91[EUR][1000 genomes]
rs12493256	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12494304	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12495221	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496784	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13099560	0.82[AFR][1000 genomes]
rs34648110	0.82[EUR][1000 genomes]
rs35142214	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4858892	0.84[EUR][1000 genomes]
rs62262998	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6442105	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6442106	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6442107	0.83[EUR][1000 genomes]
rs6442108	0.91[EUR][1000 genomes]
rs6442109	0.91[EUR][1000 genomes]
rs6766754	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6771889	0.91[EUR][1000 genomes]
rs6775114	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6797587	0.89[EUR][1000 genomes]
rs6800730	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7374376	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7429594	0.84[AMR][1000 genomes]
rs7431293	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7617773	0.91[EUR][1000 genomes]
rs9822496	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9832957	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv876760	chr3:48019258-48197614	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv834681	chr3:48032000-48181775	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1004557	chr3:48056534-48256694	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1012024	chr3:48119229-48242670	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
12	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs12494396	ZNF589	cis	Esophagus Mucosa	GTEx
rs12494396	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs12494396	CDC25A	cis	Artery Tibial	GTEx
rs12494396	MRPS18AP1	cis	Nerve Tibial	GTEx
rs12494396	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs12494396	ZNF589	cis	Artery Tibial	GTEx
rs12494396	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs12494396	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs12494396	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs12494396	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs12494396	CDC25A	cis	Thyroid	GTEx
rs12494396	ZNF589	cis	Nerve Tibial	GTEx
rs12494396	FCF1P2	cis	Artery Tibial	GTEx
rs12494396	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs12494396	NME6	cis	Esophagus Muscularis	GTEx
rs12494396	ZNF589	cis	lung	GTEx
rs12494396	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs12494396	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs12494396	CDC25A	cis	Muscle Skeletal	GTEx
rs12494396	ZNF589	cis	Thyroid	GTEx
rs12494396	MRPS18AP1	cis	Thyroid	GTEx
rs12494396	ZNF589	cis	Whole Blood	GTEx
rs12494396	ZNF589	cis	Adipose Subcutaneous	GTEx
rs12494396	MRPS18AP1	cis	lung	GTEx
rs12494396	MRPS18AP1	cis	Artery Tibial	GTEx
rs12494396	MRPS18AP1	cis	Stomach	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48167200-48178800	Weak transcription	NHEK	skin
2	chr3:48167800-48181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:48170800-48178800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:48172400-48184000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:48172800-48181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:48172800-48184000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:48173000-48181800	Weak transcription	Right Ventricle	heart
8	chr3:48173000-48181800	Weak transcription	Spleen	Spleen
9	chr3:48173200-48181600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:48173200-48181800	Weak transcription	Lung	lung
11	chr3:48177200-48178400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:48177200-48179600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:48177400-48178400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:48177600-48180200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:48177600-48181800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:48177600-48181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:48177600-48181800	Weak transcription	Fetal Kidney	kidney
18	chr3:48177800-48180200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:48177800-48181800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:48178200-48180200	Weak transcription	HepG2	liver
21	chr3:48178200-48181600	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links