Variant report

Variant	rs12787646
Chromosome Location	chr11:47669665-47669666
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47669163..47671656-chr11:47673421..47675841,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10128705	0.82[EUR][1000 genomes]
rs1064608	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838738	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838747	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838748	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838757	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039308	0.92[ASN][1000 genomes]
rs11039324	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11039342	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039348	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11039355	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039390	0.80[EUR][1000 genomes]
rs11039391	0.80[EUR][1000 genomes]
rs11602339	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11602395	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11604825	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12361031	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12363232	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12419507	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12419692	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12421210	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12787112	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12794570	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12799623	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12803191	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17788930	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2030166	0.83[AMR][1000 genomes]
rs34910028	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34923397	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35902101	0.84[EUR][1000 genomes]
rs3817334	0.95[ASN][1000 genomes]
rs3817335	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4752856	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4752857	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59360790	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66749409	0.80[ASN][1000 genomes]
rs7130758	0.87[EUR][1000 genomes]
rs7927771	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7947730	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9909	0.80[EUR][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	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12787646	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs12787646	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12787646	C1QTNF4	cis	Muscle Skeletal	GTEx
rs12787646	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs12787646	C1QTNF4	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47665000-47670000	Weak transcription	Fetal Brain Male	brain
2	chr11:47665000-47672400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:47665200-47672600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links