Variant report

Variant	rs935893
Chromosome Location	chr12:42876117-42876118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1669887	0.93[EUR][1000 genomes]
rs1669924	0.91[EUR][1000 genomes]
rs1669925	0.92[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1796339	0.92[CEU][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1796340	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs896559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs935893	PRICKLE1	cis	lymphoblastoid	seeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
2	chr12:42860200-42876200	Weak transcription	Gastric	stomach
3	chr12:42869400-42876400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:42874200-42876400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:42874400-42876400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:42874400-42876600	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr12:42874600-42876200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:42874800-42876600	Flanking Active TSS	HMEC	breast
9	chr12:42875000-42876600	Flanking Active TSS	HUVEC	blood vessel
10	chr12:42875000-42877800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr12:42875200-42876200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:42875200-42876400	Flanking Active TSS	Osteobl	bone
13	chr12:42875400-42878600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:42875400-42878800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:42875400-42878800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:42875400-42878800	Active TSS	NHLF	lung
17	chr12:42875600-42876400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:42875600-42876600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:42875800-42876200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
20	chr12:42875800-42876200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:42875800-42876200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
22	chr12:42875800-42876200	Bivalent/Poised TSS	Fetal Brain Male	brain
23	chr12:42875800-42876200	Enhancers	Stomach Mucosa	stomach
24	chr12:42875800-42876200	Flanking Active TSS	NH-A	brain
25	chr12:42875800-42876400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:42875800-42876400	Active TSS	Fetal Heart	heart
27	chr12:42875800-42876600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:42875800-42876600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:42875800-42876600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:42875800-42876600	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr12:42875800-42876600	Flanking Active TSS	HSMMtube	muscle
32	chr12:42875800-42876600	Flanking Active TSS	NHEK	skin
33	chr12:42875800-42877200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
34	chr12:42875800-42878400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr12:42875800-42878600	Active TSS	Ovary	ovary
36	chr12:42875800-42878600	Active TSS	Right Atrium	heart
37	chr12:42875800-42878600	Active TSS	Right Ventricle	heart
38	chr12:42876000-42876200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:42876000-42876200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr12:42876000-42876200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:42876000-42876200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr12:42876000-42876200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
43	chr12:42876000-42876200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr12:42876000-42876200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:42876000-42876200	Bivalent Enhancer	Liver	Liver
46	chr12:42876000-42876200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
47	chr12:42876000-42876200	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr12:42876000-42876200	Bivalent Enhancer	Fetal Intestine Large	intestine
49	chr12:42876000-42876200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
50	chr12:42876000-42876200	Flanking Active TSS	Fetal Kidney	kidney

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