Variant report

Variant	rs10880258
Chromosome Location	chr12:42547531-42547532
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	chr12:42536641..42539823-chr12:42545599..42552985,7	MCF-7	breast:
2	chr12:42535188..42540199-chr12:42545660..42549187,5	K562	blood:

Variant related genes	Relation type
ENSG00000151233	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10459290	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10492388	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1059360	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10785333	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785334	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880256	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880259	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880260	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880261	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10880264	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880268	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880269	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10880272	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880273	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181364	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11181378	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181380	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11181398	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11181399	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12049942	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12308219	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12366848	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12370778	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12371615	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12371762	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2406567	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2406568	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6582390	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6582391	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138877	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315968	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7957471	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965392	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7974476	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7974654	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9668610	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10880258	PRICKLE1	Cis_1M	lymphoblastoid	RTeQTL
rs10880258	PPHLN1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42539200-42552200	Weak transcription	HSMM	muscle
2	chr12:42539200-42563800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:42539400-42551400	Weak transcription	Primary B cells from cord blood	blood
4	chr12:42539400-42551800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:42539400-42554000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:42539400-42554200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:42539400-42556000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:42539400-42577000	Weak transcription	Aorta	Aorta
9	chr12:42539400-42583200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:42539600-42550200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:42539600-42550800	Weak transcription	Primary T cells from cord blood	blood
12	chr12:42539600-42550800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:42539600-42551600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:42539600-42551800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:42539600-42552200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr12:42539600-42552400	Weak transcription	HUVEC	blood vessel
17	chr12:42539600-42553600	Weak transcription	Adipose Nuclei	Adipose
18	chr12:42539600-42553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:42539600-42553800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:42539600-42555800	Weak transcription	Brain Substantia Nigra	brain
21	chr12:42539600-42556200	Weak transcription	HSMMtube	muscle
22	chr12:42539600-42574000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:42539600-42578400	Weak transcription	Left Ventricle	heart
24	chr12:42539600-42586000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:42539800-42550600	Weak transcription	Fetal Lung	lung
26	chr12:42539800-42550800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:42539800-42551600	Weak transcription	GM12878-XiMat	blood
28	chr12:42539800-42551800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr12:42539800-42551800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:42539800-42553000	Weak transcription	Hela-S3	cervix
31	chr12:42539800-42554200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr12:42539800-42568600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:42539800-42569000	Weak transcription	Fetal Kidney	kidney
34	chr12:42539800-42582800	Weak transcription	Spleen	Spleen
35	chr12:42539800-42607800	Weak transcription	Pancreas	Pancrea
36	chr12:42540000-42550600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:42540000-42552200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:42540000-42552200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:42540000-42553800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:42540000-42556000	Weak transcription	Fetal Intestine Small	intestine
41	chr12:42540000-42574800	Weak transcription	Brain Anterior Caudate	brain
42	chr12:42541000-42548800	Weak transcription	A549	lung
43	chr12:42541200-42553600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:42543800-42551800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:42545200-42553800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr12:42545400-42554200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:42545600-42553200	Weak transcription	NH-A	brain
48	chr12:42546000-42564400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:42546400-42553800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:42546600-42553800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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