Variant report

Variant	rs824742
Chromosome Location	chr12:42544822-42544823
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1069644	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10785335	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10880275	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1118483	0.81[EUR][1000 genomes]
rs1226298	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1238290	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1683195	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1826387	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1961953	0.84[AMR][1000 genomes]
rs2085314	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2100547	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2605401	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4402364	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4417370	0.84[EUR][1000 genomes]
rs6582385	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6582386	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6582389	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6582392	0.81[EUR][1000 genomes]
rs712108	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs712109	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs712112	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs712114	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs712115	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs712118	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs712122	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs712123	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs712125	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs712126	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs712127	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs712129	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs712130	0.81[EUR][1000 genomes]
rs7302687	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7316575	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7486516	0.84[AMR][1000 genomes]
rs7956016	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7960176	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7970115	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7975518	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs824739	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs824741	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs866091	0.88[AMR][1000 genomes];0.99[EUR][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
rs824742	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

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

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