Variant report

Variant	rs10880252
Chromosome Location	chr12:42524372-42524373
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42522464..42525193-chr12:42533031..42535242,2	K562	blood:
2	chr12:42522331..42524527-chr12:42630934..42633141,2	K562	blood:
3	chr12:42524054..42526353-chr12:42526883..42528926,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134283	Chromatin interaction
ENSG00000015153	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10492386	0.83[AMR][1000 genomes]
rs10492387	0.83[AMR][1000 genomes]
rs10785332	0.83[AMR][1000 genomes]
rs10785336	0.82[AMR][1000 genomes]
rs10880257	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10880263	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10880274	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10880276	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11181322	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11181325	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181332	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181344	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11181347	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11181348	0.83[AMR][1000 genomes]
rs11181356	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11181359	0.83[AMR][1000 genomes]
rs11181383	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11181385	0.82[AMR][1000 genomes]
rs11829883	0.82[AMR][1000 genomes]
rs11831168	0.83[AMR][1000 genomes]
rs11832197	0.83[AMR][1000 genomes]
rs12228932	0.83[AMR][1000 genomes]
rs12579560	0.81[AMR][1000 genomes]
rs12582652	0.82[AFR][1000 genomes]
rs12582890	0.80[AMR][1000 genomes]
rs1532220	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17091018	0.83[AMR][1000 genomes]
rs3852594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60631072	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61940203	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs61940227	0.83[AMR][1000 genomes]
rs61942482	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61942484	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73116436	0.82[AFR][1000 genomes]
rs7485381	0.82[AFR][1000 genomes]
rs7960726	0.80[AFR][1000 genomes]
rs7965273	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7972986	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7978820	0.83[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
rs10880252	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42471800-42524400	Weak transcription	Esophagus	oesophagus
2	chr12:42476000-42524400	Weak transcription	Gastric	stomach
3	chr12:42476200-42524400	Weak transcription	Pancreas	Pancrea
4	chr12:42484400-42524800	Weak transcription	Right Ventricle	heart
5	chr12:42493000-42524400	Weak transcription	Brain Substantia Nigra	brain
6	chr12:42493000-42534400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:42505800-42537000	Weak transcription	Fetal Stomach	stomach
8	chr12:42505800-42537000	Weak transcription	Lung	lung
9	chr12:42508400-42524600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:42512000-42537400	Weak transcription	Ovary	ovary
11	chr12:42512400-42537000	Weak transcription	Placenta	Placenta
12	chr12:42512600-42524400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:42512600-42524600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:42512800-42524400	Weak transcription	Left Ventricle	heart
15	chr12:42513000-42537000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr12:42513200-42537200	Weak transcription	Primary T cells from cord blood	blood
17	chr12:42519000-42524800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:42519000-42537000	Weak transcription	Right Atrium	heart
19	chr12:42519200-42524400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:42519200-42524600	Enhancers	A549	lung
21	chr12:42519200-42524600	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:42519200-42529000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:42519200-42537400	Weak transcription	Small Intestine	intestine
24	chr12:42519400-42524600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr12:42519400-42524600	Weak transcription	Adipose Nuclei	Adipose
26	chr12:42519600-42524400	Weak transcription	Psoas Muscle	Psoas
27	chr12:42519600-42524600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:42519600-42526600	Weak transcription	HepG2	liver
29	chr12:42519600-42528400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:42519600-42537200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:42519800-42524600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:42519800-42529000	Weak transcription	GM12878-XiMat	blood
33	chr12:42519800-42536800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr12:42519800-42537000	Weak transcription	Primary B cells from cord blood	blood
35	chr12:42520000-42524400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:42522600-42537000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:42522800-42524400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:42522800-42528400	Weak transcription	Fetal Intestine Small	intestine
39	chr12:42523000-42524600	Weak transcription	Stomach Mucosa	stomach
40	chr12:42523600-42524400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr12:42523600-42525600	Enhancers	HUVEC	blood vessel
42	chr12:42523600-42525800	Enhancers	Liver	Liver
43	chr12:42523800-42524400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:42523800-42524400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:42523800-42524400	Enhancers	HMEC	breast
46	chr12:42523800-42524400	Enhancers	NHEK	skin
47	chr12:42523800-42524600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:42523800-42524600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr12:42523800-42524600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr12:42523800-42524600	Enhancers	HSMM	muscle

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