Variant report

Variant	rs11181344
Chromosome Location	chr12:42534085-42534086
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42533596..42535148-chr12:42538316..42539822,2	K562	blood:
2	chr12:42531740..42536122-chr12:42718714..42721599,4	MCF-7	breast:
3	chr12:42526307..42530299-chr12:42534078..42537991,4	K562	blood:
4	chr12:42522464..42525193-chr12:42533031..42535242,2	K562	blood:
5	chr12:42527145..42529069-chr12:42534078..42535824,2	K562	blood:

Variant related genes	Relation type
ENSG00000151233	Chromatin interaction
ENSG00000139168	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10492386	0.93[JPT][hapmap];0.81[AMR][1000 genomes]
rs10492387	0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs10785332	0.93[JPT][hapmap];0.81[AMR][1000 genomes]
rs10785336	0.80[AMR][1000 genomes]
rs10880252	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880257	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10880263	0.93[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10880274	0.93[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10880276	0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10880285	0.86[JPT][hapmap]
rs10880286	0.84[YRI][hapmap]
rs11181322	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11181325	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181347	0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11181348	0.81[AMR][1000 genomes]
rs11181356	0.93[JPT][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11181359	0.93[JPT][hapmap];0.81[AMR][1000 genomes]
rs11181383	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11181384	0.93[JPT][hapmap]
rs11181385	0.80[AMR][1000 genomes]
rs11181388	0.93[JPT][hapmap]
rs11181426	0.86[JPT][hapmap]
rs11181430	0.90[JPT][hapmap]
rs11829883	0.80[AMR][1000 genomes]
rs11831168	0.81[AMR][1000 genomes]
rs11832197	0.81[AMR][1000 genomes]
rs12228932	0.81[AMR][1000 genomes]
rs12579560	0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs12581958	0.92[JPT][hapmap]
rs12582652	0.82[AFR][1000 genomes]
rs1532220	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17091018	0.93[JPT][hapmap];0.81[AMR][1000 genomes]
rs1988893	0.93[JPT][hapmap]
rs3810786	0.86[JPT][hapmap]
rs3810788	0.86[JPT][hapmap];0.84[YRI][hapmap]
rs3810789	0.86[JPT][hapmap]
rs3810790	0.86[JPT][hapmap]
rs3852593	0.82[JPT][hapmap]
rs3852594	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60631072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61940203	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs61940227	0.81[AMR][1000 genomes]
rs61942482	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61942484	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7296847	0.86[JPT][hapmap]
rs73116436	0.82[AFR][1000 genomes]
rs7485381	0.82[AFR][1000 genomes]
rs7960726	0.80[AFR][1000 genomes]
rs7965273	0.86[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7972986	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7978820	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11181344	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42493000-42534400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:42505800-42537000	Weak transcription	Fetal Stomach	stomach
3	chr12:42505800-42537000	Weak transcription	Lung	lung
4	chr12:42512000-42537400	Weak transcription	Ovary	ovary
5	chr12:42512400-42537000	Weak transcription	Placenta	Placenta
6	chr12:42513000-42537000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:42513200-42537200	Weak transcription	Primary T cells from cord blood	blood
8	chr12:42519000-42537000	Weak transcription	Right Atrium	heart
9	chr12:42519200-42537400	Weak transcription	Small Intestine	intestine
10	chr12:42519600-42537200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:42519800-42536800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:42519800-42537000	Weak transcription	Primary B cells from cord blood	blood
13	chr12:42522600-42537000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:42524000-42537200	Weak transcription	Aorta	Aorta
15	chr12:42524600-42537000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:42524800-42537000	Weak transcription	Fetal Kidney	kidney
17	chr12:42524800-42537000	Weak transcription	Gastric	stomach
18	chr12:42524800-42537200	Weak transcription	Left Ventricle	heart
19	chr12:42524800-42537200	Weak transcription	Psoas Muscle	Psoas
20	chr12:42525400-42535800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:42525600-42534800	Weak transcription	HSMM	muscle
22	chr12:42525600-42536800	Weak transcription	HUVEC	blood vessel
23	chr12:42529000-42534400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:42529000-42537000	Weak transcription	Fetal Intestine Small	intestine
25	chr12:42529200-42534400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:42529200-42534400	Weak transcription	NH-A	brain
27	chr12:42529600-42534400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:42529600-42534600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:42529600-42534600	Weak transcription	Osteobl	bone
30	chr12:42529600-42535600	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr12:42529600-42537000	Weak transcription	NHLF	lung
32	chr12:42529800-42534600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr12:42529800-42534600	Weak transcription	NHDF-Ad	bronchial
34	chr12:42529800-42536600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:42529800-42537000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:42530000-42534600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:42530000-42535800	Weak transcription	Hela-S3	cervix
38	chr12:42530200-42534600	Weak transcription	NHEK	skin
39	chr12:42530400-42534400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:42530400-42534400	Weak transcription	HMEC	breast
41	chr12:42530400-42534600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:42530600-42534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:42531000-42534800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:42531600-42537200	Weak transcription	Right Ventricle	heart
45	chr12:42531800-42537200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:42532000-42534600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:42532000-42536400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr12:42532000-42537000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:42532000-42537000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr12:42532000-42537400	Weak transcription	Fetal Muscle Trunk	muscle

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