Variant report

Variant	rs2053946
Chromosome Location	chr12:42864514-42864515
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:42856522..42859149-chr12:42861270..42865700,4	K562	blood:
2	chr12:42858889..42861856-chr12:42862365..42864970,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

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

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42831800-42876400	Weak transcription	Psoas Muscle	Psoas
2	chr12:42836000-42875800	Weak transcription	Stomach Mucosa	stomach
3	chr12:42837000-42868800	Weak transcription	Esophagus	oesophagus
4	chr12:42849400-42864800	Strong transcription	Fetal Stomach	stomach
5	chr12:42850000-42866400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:42850200-42865000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:42850200-42865000	Strong transcription	Fetal Muscle Trunk	muscle
8	chr12:42850200-42865800	Strong transcription	Osteobl	bone
9	chr12:42853400-42869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:42854000-42865800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:42854000-42868600	Weak transcription	Right Ventricle	heart
12	chr12:42854200-42865200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:42854200-42867400	Weak transcription	NHLF	lung
14	chr12:42854400-42864800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:42854400-42865200	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr12:42854600-42864800	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr12:42855400-42865200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:42856200-42865800	Strong transcription	HMEC	breast
19	chr12:42859200-42864800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:42859200-42865200	Weak transcription	Fetal Intestine Small	intestine
21	chr12:42860200-42866800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:42860200-42868800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr12:42860200-42870400	Weak transcription	Pancreas	Pancrea
24	chr12:42860200-42876200	Weak transcription	Gastric	stomach
25	chr12:42860800-42864600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:42861400-42876000	Weak transcription	Lung	lung
27	chr12:42861600-42866200	Weak transcription	Ovary	ovary
28	chr12:42862000-42865800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr12:42862200-42865200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:42862400-42866000	Strong transcription	HSMMtube	muscle
31	chr12:42862400-42867200	Genic enhancers	HUVEC	blood vessel
32	chr12:42862400-42867400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:42862800-42864600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:42862800-42876000	Weak transcription	Aorta	Aorta
35	chr12:42863200-42865600	Strong transcription	HSMM	muscle
36	chr12:42863200-42868400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:42863200-42868800	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:42863400-42864800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:42863400-42864800	Weak transcription	Brain Angular Gyrus	brain
40	chr12:42863400-42865200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:42863400-42866000	Weak transcription	Placenta	Placenta
42	chr12:42863400-42866200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:42863400-42866200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:42863400-42866200	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr12:42863400-42866200	Weak transcription	Right Atrium	heart
46	chr12:42863400-42866200	Strong transcription	NH-A	brain
47	chr12:42863400-42866600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr12:42863400-42866600	Weak transcription	NHEK	skin
49	chr12:42863400-42866800	Strong transcription	Fetal Muscle Leg	muscle
50	chr12:42863400-42866800	Weak transcription	Stomach Smooth Muscle	stomach

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