Variant report

Variant	rs2708063
Chromosome Location	chr12:42813317-42813318
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42630503..42634149-chr12:42810958..42813729,3	K562	blood:
2	chr12:42802234..42803947-chr12:42811454..42813623,2	K562	blood:

Variant related genes	Relation type
ENSG00000015153	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1043652	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1043656	0.91[EUR][1000 genomes]
rs10880282	0.88[EUR][1000 genomes]
rs10880284	0.89[EUR][1000 genomes]
rs11181421	0.92[EUR][1000 genomes]
rs11181427	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11181453	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11181484	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12229224	0.96[EUR][1000 genomes]
rs12229266	0.91[EUR][1000 genomes]
rs12230583	0.91[EUR][1000 genomes]
rs12231335	0.89[EUR][1000 genomes]
rs12422938	0.90[EUR][1000 genomes]
rs12423383	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12425945	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12578312	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1376931	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1629725	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669884	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669888	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1669890	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669891	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669895	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669897	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1669899	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669901	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669903	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669911	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669912	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1669913	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1669914	1.00[EUR][1000 genomes]
rs1669935	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17091052	0.83[EUR][1000 genomes]
rs1796354	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1796355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796357	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796359	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1796360	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1796365	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796374	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796377	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796379	0.99[EUR][1000 genomes]
rs1796385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1796387	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796389	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796392	0.93[EUR][1000 genomes]
rs1796395	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796396	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1796397	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1796398	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1961953	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2053946	0.89[EUR][1000 genomes]
rs2061191	0.81[EUR][1000 genomes]
rs2243465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2406872	0.89[EUR][1000 genomes]
rs2406969	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2600911	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2600912	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2600916	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2600917	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2600918	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2708069	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2708075	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2708077	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2708506	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2952653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213989	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3747563	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3761677	0.89[EUR][1000 genomes]
rs3827524	0.98[EUR][1000 genomes]
rs4603368	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768397	0.89[EUR][1000 genomes]
rs4768398	0.88[EUR][1000 genomes]
rs4768401	0.99[EUR][1000 genomes]
rs4768412	0.89[EUR][1000 genomes]
rs7134895	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs721447	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7298965	0.81[EUR][1000 genomes]
rs73122408	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73122414	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73122418	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7486516	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs752767	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs896555	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs896556	0.82[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
rs2708063	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42738200-42823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:42767200-42836200	Weak transcription	Esophagus	oesophagus
4	chr12:42770200-42815800	Weak transcription	Fetal Lung	lung
5	chr12:42770400-42816600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr12:42780200-42836000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:42783000-42836000	Weak transcription	Lung	lung
8	chr12:42785400-42836000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:42789600-42836200	Weak transcription	Pancreas	Pancrea
10	chr12:42793800-42840400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:42795000-42813600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr12:42795400-42834600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:42795600-42820400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:42795600-42820600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:42795600-42825800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:42795600-42834400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:42795800-42821800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:42795800-42836000	Weak transcription	Thymus	Thymus
19	chr12:42796000-42813400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:42796000-42819600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:42796000-42820400	Weak transcription	NHEK	skin
22	chr12:42796000-42823600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:42796000-42825600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:42796000-42825800	Weak transcription	Left Ventricle	heart
25	chr12:42796000-42833200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:42796000-42834400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:42796000-42835000	Weak transcription	HepG2	liver
28	chr12:42796000-42835800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:42796000-42836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:42796000-42836200	Weak transcription	Fetal Stomach	stomach
31	chr12:42796000-42836400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:42796000-42838000	Weak transcription	HSMMtube	muscle
33	chr12:42796200-42813600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:42796200-42826000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:42796400-42813800	Weak transcription	GM12878-XiMat	blood
36	chr12:42796400-42815400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:42797000-42813400	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr12:42797000-42815800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:42797000-42820600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:42799600-42813600	Weak transcription	Hela-S3	cervix
41	chr12:42799600-42815600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:42799600-42816000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:42799800-42820600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:42799800-42825400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:42801000-42814800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:42801200-42823200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr12:42801400-42815400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:42801400-42817800	Weak transcription	Dnd41	blood
49	chr12:42801400-42825800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr12:42801600-42813400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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