Variant report

Variant	rs13064576
Chromosome Location	chr3:49642430-49642431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10212296	0.84[EUR][1000 genomes]
rs11130203	0.86[EUR][1000 genomes]
rs11130213	0.82[AMR][1000 genomes]
rs1131095	0.82[AMR][1000 genomes]
rs11709525	0.84[AMR][1000 genomes]
rs11710037	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11712569	0.81[EUR][1000 genomes]
rs11713474	0.88[EUR][1000 genomes]
rs11718165	0.82[AMR][1000 genomes]
rs11719996	0.83[EUR][1000 genomes]
rs11720597	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11917431	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11921590	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11926781	0.89[EUR][1000 genomes]
rs12330269	0.84[EUR][1000 genomes]
rs13079082	0.89[EUR][1000 genomes]
rs13085791	0.84[AMR][1000 genomes]
rs13316695	0.86[AMR][1000 genomes]
rs1352890	0.81[ASN][1000 genomes]
rs1801143	0.89[EUR][1000 genomes]
rs1873625	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2172252	0.85[AMR][1000 genomes]
rs3197999	0.81[AMR][1000 genomes]
rs34196454	0.85[EUR][1000 genomes]
rs34293138	0.89[EUR][1000 genomes]
rs34363169	0.84[EUR][1000 genomes]
rs34427167	0.89[EUR][1000 genomes]
rs34762726	0.86[AMR][1000 genomes]
rs35261698	0.84[EUR][1000 genomes]
rs35999162	0.88[EUR][1000 genomes]
rs3811697	0.89[EUR][1000 genomes]
rs3926569	0.85[EUR][1000 genomes]
rs4283605	0.86[AMR][1000 genomes]
rs4625	0.87[EUR][1000 genomes]
rs6766131	0.84[EUR][1000 genomes]
rs6766581	0.84[EUR][1000 genomes]
rs6770670	0.85[AMR][1000 genomes]
rs6797664	0.84[EUR][1000 genomes]
rs6803222	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7614725	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7622302	0.85[EUR][1000 genomes]
rs7630869	0.83[EUR][1000 genomes]
rs7633271	0.85[EUR][1000 genomes]
rs9812791	0.86[AMR][1000 genomes]
rs9818590	0.84[EUR][1000 genomes]
rs9821311	0.85[EUR][1000 genomes]
rs9822268	0.84[AMR][1000 genomes]
rs9823546	0.82[AMR][1000 genomes]
rs9824092	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9827021	0.84[EUR][1000 genomes]
rs9827708	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9833611	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9836291	0.82[AMR][1000 genomes]
rs9837027	0.89[EUR][1000 genomes]
rs9837341	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9850072	0.84[EUR][1000 genomes]
rs9853683	0.84[EUR][1000 genomes]
rs9858280	0.89[EUR][1000 genomes]
rs9858418	0.82[EUR][1000 genomes]
rs9858542	0.82[AMR][1000 genomes]
rs9862080	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9875617	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9882740	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv3324697	chr3:49641773-49644321	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
3	esv3356519	chr3:49642123-49644746	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
4	esv3371128	chr3:49642398-49644346	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13064576	FAM212A	cis	Muscle Skeletal	GTEx
rs13064576	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs13064576	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49637800-49653600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49638000-49644600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:49638000-49647200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:49639200-49643800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:49639800-49644000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:49639800-49644000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:49639800-49644600	Weak transcription	NHDF-Ad	bronchial
8	chr3:49640400-49646800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr3:49640600-49644000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:49640600-49644200	Weak transcription	Hela-S3	cervix
11	chr3:49640600-49644800	Weak transcription	Brain Angular Gyrus	brain
12	chr3:49640600-49647000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:49640800-49646800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:49641000-49643800	Weak transcription	Spleen	Spleen
15	chr3:49641000-49644000	Weak transcription	Pancreas	Pancrea
16	chr3:49641000-49644600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:49641200-49644400	Weak transcription	HMEC	breast
18	chr3:49641200-49644400	Weak transcription	NHEK	skin
19	chr3:49641200-49644600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:49641200-49653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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