Variant report

Variant	rs73088791
Chromosome Location	chr3:52318281-52318282
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52318055-52318330	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52317008..52318750-chr3:52319052..52321933,3	MCF-7	breast:
2	chr3:52312154..52315273-chr3:52316088..52318797,4	K562	blood:
3	chr3:52311051..52315983-chr3:52317623..52323290,10	MCF-7	breast:
4	chr3:52298716..52301587-chr3:52317190..52319197,2	K562	blood:
5	chr3:52317125..52319496-chr3:52319751..52323578,5	K562	blood:

Variant related genes	Relation type
GLYCTK	TF binding region
ENSG00000168237	Chromatin interaction
ENSG00000164091	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10460962	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461027	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461028	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865971	0.83[EUR][1000 genomes]
rs11706515	0.94[EUR][1000 genomes]
rs11706541	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11707056	1.00[EUR][1000 genomes]
rs11708581	0.94[EUR][1000 genomes]
rs11708811	1.00[EUR][1000 genomes]
rs11710014	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11711914	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11711974	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11713464	0.83[AMR][1000 genomes]
rs11713914	0.94[EUR][1000 genomes]
rs11714358	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11715208	1.00[EUR][1000 genomes]
rs11715382	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11715391	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11717028	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11718729	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11719760	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11720365	0.94[EUR][1000 genomes]
rs11721277	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052051	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052052	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17052053	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052054	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17263770	0.81[EUR][1000 genomes]
rs1767	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1769	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35976326	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733063	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3886875	0.88[EUR][1000 genomes]
rs4082828	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55676974	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55806905	0.94[EUR][1000 genomes]
rs55813842	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55847657	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56002041	0.94[EUR][1000 genomes]
rs56322342	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56352611	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56899118	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57849650	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58531656	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58879205	0.83[AMR][1000 genomes]
rs60382084	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61644644	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445385	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6776759	0.81[EUR][1000 genomes]
rs6783652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793317	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809248	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs724801	0.82[EUR][1000 genomes]
rs729555	0.82[EUR][1000 genomes]
rs73072990	0.88[EUR][1000 genomes]
rs73088773	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73088783	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088785	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088800	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091166	0.94[EUR][1000 genomes]
rs73091168	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs746239	0.94[EUR][1000 genomes]
rs7615405	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7628461	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7633687	0.94[EUR][1000 genomes]
rs7638204	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7643913	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73088791	PPM1M	cis	Artery Tibial	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52313200-52321000	Weak transcription	Gastric	stomach
2	chr3:52313400-52320400	Weak transcription	Lung	lung
3	chr3:52313400-52321000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:52313600-52320800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:52313600-52320800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:52313600-52320800	Weak transcription	Colonic Mucosa	Colon
7	chr3:52313600-52321000	Enhancers	Fetal Intestine Large	intestine
8	chr3:52313600-52321000	Weak transcription	Left Ventricle	heart
9	chr3:52313600-52321000	Weak transcription	Psoas Muscle	Psoas
10	chr3:52313600-52321000	Weak transcription	Right Atrium	heart
11	chr3:52313800-52318600	Enhancers	Primary T cells fromperipheralblood	blood
12	chr3:52313800-52320800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:52313800-52320800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:52314000-52320800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:52314000-52320800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:52314000-52321000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:52314200-52320800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:52314200-52320800	Weak transcription	Fetal Brain Female	brain
19	chr3:52314200-52320800	Weak transcription	NHLF	lung
20	chr3:52314400-52320400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:52314400-52320600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:52314400-52320600	Weak transcription	Dnd41	blood
23	chr3:52314400-52320800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:52314400-52320800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:52314400-52320800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:52314400-52320800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:52314400-52320800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:52314400-52320800	Weak transcription	Brain Substantia Nigra	brain
29	chr3:52314400-52320800	Weak transcription	HMEC	breast
30	chr3:52314400-52320800	Weak transcription	NHEK	skin
31	chr3:52314400-52321000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:52314600-52318800	Weak transcription	Stomach Mucosa	stomach
33	chr3:52314600-52320600	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:52314600-52320800	Weak transcription	Brain Anterior Caudate	brain
35	chr3:52314600-52320800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:52314600-52320800	Weak transcription	Fetal Lung	lung
37	chr3:52314600-52321000	Weak transcription	Brain Germinal Matrix	brain
38	chr3:52314800-52320400	Weak transcription	Pancreas	Pancrea
39	chr3:52314800-52320400	Weak transcription	HSMM	muscle
40	chr3:52314800-52320600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:52314800-52320800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:52314800-52320800	Weak transcription	Brain Angular Gyrus	brain
43	chr3:52314800-52320800	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:52314800-52320800	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:52314800-52320800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:52314800-52320800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:52314800-52321000	Weak transcription	Right Ventricle	heart
48	chr3:52315400-52318400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:52315600-52318400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:52315600-52318600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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