Variant report

Variant	rs73088800
Chromosome Location	chr3:52332292-52332293
allele	A/G
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	chr3:52327536-52335341	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:52332279-52332934	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:52326828-52335551	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:52330489-52334598	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:52326795-52334549	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:52332066-52332307	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:52326721-52333108	HepG2	liver:	n/a	n/a
8	REST	chr3:52331995-52334516	H1-neurons	neurons:	n/a	chr3:52334239-52334252 chr3:52334242-52334255 chr3:52334249-52334259 chr3:52332509-52332529 chr3:52334190-52334203 chr3:52332675-52332685 chr3:52334119-52334132
9	POLR2A	chr3:52332268-52332453	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52328227..52330124-chr3:52332267..52334731,2	MCF-7	breast:
2	chr3:52330648..52332485-chr3:52338517..52342537,3	K562	blood:
3	chr3:52331076..52332761-chr3:52353981..52355640,2	K562	blood:

Variant related genes	Relation type
MIR135A1	TF binding region
ENSG00000207926	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10460962	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10461027	0.93[EUR][1000 genomes]
rs10461028	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11706001	0.82[AFR][1000 genomes]
rs11706515	0.90[EUR][1000 genomes]
rs11706541	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707056	0.96[EUR][1000 genomes]
rs11707931	0.92[AFR][1000 genomes]
rs11708581	0.90[EUR][1000 genomes]
rs11708811	0.96[EUR][1000 genomes]
rs11710014	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11711914	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11711934	0.93[AFR][1000 genomes]
rs11711974	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11713914	0.90[EUR][1000 genomes]
rs11714313	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11714358	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11715208	0.96[EUR][1000 genomes]
rs11715382	0.87[EUR][1000 genomes]
rs11715391	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11717028	0.93[EUR][1000 genomes]
rs11717574	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11718729	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719760	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720365	0.90[EUR][1000 genomes]
rs11721277	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13059674	0.96[AFR][1000 genomes]
rs17052051	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052052	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052054	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052058	0.95[AFR][1000 genomes]
rs17052061	0.95[AFR][1000 genomes]
rs17052068	0.95[AFR][1000 genomes]
rs1767	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2335640	0.93[AFR][1000 genomes]
rs34238085	0.96[AFR][1000 genomes]
rs34523877	0.96[AFR][1000 genomes]
rs34762015	0.94[AFR][1000 genomes]
rs35133416	0.92[AFR][1000 genomes]
rs35976326	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3733063	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852062	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3886875	0.84[EUR][1000 genomes]
rs4082828	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55676974	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55806905	0.90[EUR][1000 genomes]
rs55813842	0.90[EUR][1000 genomes]
rs55847657	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55965068	0.93[AFR][1000 genomes]
rs55997317	0.95[AFR][1000 genomes]
rs56002041	0.90[EUR][1000 genomes]
rs56322342	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56352611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56357549	0.94[AFR][1000 genomes]
rs56899118	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57441156	0.89[AFR][1000 genomes]
rs57849650	0.90[EUR][1000 genomes]
rs58531656	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60382084	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61150019	0.95[AFR][1000 genomes]
rs61644644	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61729402	1.00[ASN][1000 genomes]
rs61729450	1.00[ASN][1000 genomes]
rs6445385	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6445386	0.95[AFR][1000 genomes]
rs6763882	0.91[AFR][1000 genomes]
rs6783652	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6793317	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796333	0.93[AFR][1000 genomes]
rs6809248	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73072990	0.84[EUR][1000 genomes]
rs73088773	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73088783	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088785	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088791	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091166	0.90[EUR][1000 genomes]
rs73091168	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs746239	0.90[EUR][1000 genomes]
rs7615405	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628461	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7633687	0.90[EUR][1000 genomes]
rs7638204	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7643913	0.83[AMR][1000 genomes];0.96[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs73088800	PPM1M	cis	Artery Tibial	GTEx
rs73088800	PPM1M	cis	Nerve Tibial	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52322600-52334400	Weak transcription	NHDF-Ad	bronchial
2	chr3:52323000-52332600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
4	chr3:52323400-52333200	Weak transcription	HUVEC	blood vessel
5	chr3:52324000-52332800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:52325600-52340400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:52327200-52332600	Weak transcription	Left Ventricle	heart
8	chr3:52327200-52333200	Weak transcription	GM12878-XiMat	blood
9	chr3:52327200-52333800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
11	chr3:52327400-52338400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
13	chr3:52327600-52334000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:52327600-52344600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:52327800-52333200	Weak transcription	Colonic Mucosa	Colon
16	chr3:52327800-52333800	Weak transcription	Esophagus	oesophagus
17	chr3:52328000-52333000	Enhancers	Liver	Liver
18	chr3:52328000-52334200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:52328000-52337000	Weak transcription	Adipose Nuclei	Adipose
20	chr3:52328000-52347000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:52328200-52332800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:52328200-52333200	Weak transcription	Gastric	stomach
23	chr3:52328200-52334200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:52328200-52340200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
26	chr3:52328600-52340000	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:52328800-52340200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
29	chr3:52329000-52334400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:52329600-52332800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:52330000-52335000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:52330200-52334600	Enhancers	Primary hematopoietic stem cells	blood
34	chr3:52330200-52343400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:52330200-52343400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:52330200-52345400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:52330600-52333600	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:52330800-52332600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
40	chr3:52331000-52337600	Weak transcription	Primary T cells from cord blood	blood
41	chr3:52331000-52343200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:52331200-52334200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:52331200-52335200	Enhancers	Duodenum Mucosa	Duodenum
44	chr3:52331200-52342800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr3:52331400-52332400	Enhancers	Fetal Lung	lung
46	chr3:52331400-52332400	Enhancers	Pancreas	Pancrea
47	chr3:52331400-52332600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
48	chr3:52331400-52332800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:52331400-52333400	Enhancers	Primary T cells fromperipheralblood	blood
50	chr3:52331400-52333800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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