Variant report

Variant	rs11181317
Chromosome Location	chr12:42471931-42471932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:42471631-42472389	K562	blood:	n/a	n/a
2	POLR2A	chr12:42471630-42472118	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000222884	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10880222	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11181282	0.82[AMR][1000 genomes]
rs11181283	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11181322	0.86[AMR][1000 genomes]
rs11181325	0.86[AMR][1000 genomes]
rs11181332	0.86[AMR][1000 genomes]
rs12231330	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1532220	0.81[AMR][1000 genomes]
rs17090898	0.96[AMR][1000 genomes]
rs17494245	0.90[AMR][1000 genomes]
rs3864939	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56085053	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs61942479	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61942482	0.86[AMR][1000 genomes]
rs61942484	0.86[AMR][1000 genomes]
rs7315650	0.98[ASN][1000 genomes]
rs7972986	0.89[AMR][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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1047830	chr12:42466192-42497603	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11181317	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42463800-42474600	Weak transcription	Left Ventricle	heart
2	chr12:42464600-42484000	Weak transcription	HSMM	muscle
3	chr12:42468400-42490200	Weak transcription	Spleen	Spleen
4	chr12:42469400-42491800	Weak transcription	Ovary	ovary
5	chr12:42470400-42479200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:42470400-42484000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:42470600-42475000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:42470600-42476000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr12:42470600-42484000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:42470600-42491400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:42470800-42480000	Weak transcription	A549	lung
12	chr12:42470800-42485600	Weak transcription	Aorta	Aorta
13	chr12:42471000-42504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:42471200-42472000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:42471200-42479000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:42471200-42483400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:42471400-42485600	Weak transcription	Fetal Muscle Leg	muscle
18	chr12:42471800-42483400	Weak transcription	Fetal Stomach	stomach
19	chr12:42471800-42486600	Weak transcription	Fetal Intestine Small	intestine
20	chr12:42471800-42524400	Weak transcription	Esophagus	oesophagus

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