Variant report

Variant	rs1629725
Chromosome Location	chr12:42769348-42769349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1043652	0.92[EUR][1000 genomes]
rs1043656	0.91[EUR][1000 genomes]
rs10880282	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880284	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181421	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11181427	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11181453	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11181461	0.97[ASN][1000 genomes]
rs11181484	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229224	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][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	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12425945	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12578312	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1376931	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669884	0.93[EUR][1000 genomes]
rs1669888	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1669890	0.98[EUR][1000 genomes]
rs1669891	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1669894	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669895	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669897	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669898	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669899	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1669900	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669901	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669903	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669905	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669911	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669912	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669913	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669914	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1669935	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1669937	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17091052	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1796354	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796355	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796356	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796357	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796359	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796360	0.99[EUR][1000 genomes]
rs1796365	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796373	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796374	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796377	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796379	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796385	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1796387	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796389	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796392	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796395	0.97[EUR][1000 genomes]
rs1796396	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1796397	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796398	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1961953	0.83[EUR][1000 genomes]
rs2053946	0.89[EUR][1000 genomes]
rs2061191	0.81[EUR][1000 genomes]
rs2243465	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2406872	0.89[EUR][1000 genomes]
rs2406969	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2600911	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2600912	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2600916	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2600917	0.90[EUR][1000 genomes]
rs2600918	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2708063	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2708069	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708075	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2708077	0.92[EUR][1000 genomes]
rs2708506	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952653	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3213989	0.88[EUR][1000 genomes]
rs3747563	0.91[EUR][1000 genomes]
rs3761677	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3827524	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4603368	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768397	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768398	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768401	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768412	0.89[EUR][1000 genomes]
rs7134895	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs721447	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7298965	0.81[EUR][1000 genomes]
rs73122408	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73122414	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73122418	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7486516	0.83[EUR][1000 genomes]
rs752767	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs896555	0.97[EUR][1000 genomes]
rs896556	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	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
3	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
rs1629725	PPHLN1	cis	Artery Tibial	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42721600-42778600	Weak transcription	Spleen	Spleen
3	chr12:42721600-42800800	Weak transcription	Psoas Muscle	Psoas
4	chr12:42721600-42803600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:42721800-42769600	Weak transcription	Brain Substantia Nigra	brain
6	chr12:42721800-42769800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr12:42721800-42797000	Weak transcription	NHLF	lung
8	chr12:42721800-42803600	Weak transcription	Gastric	stomach
9	chr12:42722000-42769600	Weak transcription	Brain Anterior Caudate	brain
10	chr12:42722000-42769600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:42722000-42772600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:42722000-42793200	Weak transcription	Fetal Kidney	kidney
13	chr12:42730800-42769600	Weak transcription	NH-A	brain
14	chr12:42731400-42769600	Weak transcription	Fetal Lung	lung
15	chr12:42731800-42770400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:42732200-42781200	Weak transcription	Fetal Brain Female	brain
17	chr12:42732200-42794400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:42732400-42769600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr12:42733400-42796800	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:42738000-42787400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr12:42738200-42823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:42746000-42778400	Weak transcription	Fetal Brain Male	brain
23	chr12:42746600-42769800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr12:42750400-42769400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:42750400-42769600	Weak transcription	HSMMtube	muscle
26	chr12:42750400-42770200	Weak transcription	Fetal Muscle Leg	muscle
27	chr12:42750400-42770200	Weak transcription	Fetal Stomach	stomach
28	chr12:42750400-42770200	Weak transcription	Thymus	Thymus
29	chr12:42750600-42769400	Weak transcription	Placenta	Placenta
30	chr12:42750800-42769800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:42752000-42769400	Weak transcription	Adipose Nuclei	Adipose
32	chr12:42753600-42776200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:42754400-42769800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:42756200-42769400	Weak transcription	Hela-S3	cervix
35	chr12:42756600-42769400	Weak transcription	HSMM	muscle
36	chr12:42757000-42769400	Weak transcription	HMEC	breast
37	chr12:42757000-42769600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr12:42757000-42769600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:42759000-42770000	Weak transcription	HepG2	liver
40	chr12:42759000-42780000	Weak transcription	Stomach Mucosa	stomach
41	chr12:42759400-42783200	Weak transcription	A549	lung
42	chr12:42759600-42778400	Weak transcription	K562	blood
43	chr12:42761000-42779000	Weak transcription	Fetal Heart	heart
44	chr12:42761200-42782200	Weak transcription	Lung	lung
45	chr12:42761800-42778400	Weak transcription	Brain Germinal Matrix	brain
46	chr12:42762800-42778600	Weak transcription	Right Ventricle	heart
47	chr12:42763400-42769600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:42763400-42778400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:42763800-42778400	Weak transcription	NHEK	skin
50	chr12:42763800-42804200	Weak transcription	Colon Smooth Muscle	Colon

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