Variant report

Variant	rs73088783
Chromosome Location	chr3:52305286-52305287
allele	C/T
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	BHLHE40	chr3:52305032-52305765	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:52305210-52305497	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52304087..52306795-chr3:52318600..52320906,2	K562	blood:
2	chr3:52292200..52293754-chr3:52305089..52307890,2	MCF-7	breast:
3	chr3:52304279..52306605-chr3:52344812..52346956,2	K562	blood:
4	chr3:52304494..52307260-chr3:52321098..52323365,4	K562	blood:

Variant related genes	Relation type
WDR82	TF binding region
MIRLET7G	TF binding region
ENSG00000164091	Chromatin interaction
ENSG00000168237	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10460962	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10461027	0.93[EUR][1000 genomes]
rs10461028	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11706515	0.90[EUR][1000 genomes]
rs11706541	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707056	0.96[EUR][1000 genomes]
rs11708581	0.90[EUR][1000 genomes]
rs11708811	0.96[EUR][1000 genomes]
rs11710014	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11711914	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11711974	0.90[EUR][1000 genomes]
rs11713914	0.90[EUR][1000 genomes]
rs11714313	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11714358	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11715208	0.96[EUR][1000 genomes]
rs11715382	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11715391	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11717028	0.93[EUR][1000 genomes]
rs11717574	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11718125	0.80[AFR][1000 genomes]
rs11718729	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719760	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720365	0.90[EUR][1000 genomes]
rs11721277	0.90[EUR][1000 genomes]
rs17052051	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052052	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052053	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17052054	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1767	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1769	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35976326	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3733063	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852062	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3886875	0.84[EUR][1000 genomes]
rs4082828	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55676974	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55806905	0.90[EUR][1000 genomes]
rs55813842	0.90[EUR][1000 genomes]
rs55847657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56002041	0.90[EUR][1000 genomes]
rs56322342	0.90[EUR][1000 genomes]
rs56352611	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56899118	0.90[EUR][1000 genomes]
rs57849650	0.90[EUR][1000 genomes]
rs58531656	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60382084	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61644644	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61729402	1.00[ASN][1000 genomes]
rs61729450	1.00[ASN][1000 genomes]
rs6445385	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6783652	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6793317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73072990	0.84[EUR][1000 genomes]
rs73088773	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73088785	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088791	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088800	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73091166	0.90[EUR][1000 genomes]
rs73091168	0.90[EUR][1000 genomes]
rs746239	0.90[EUR][1000 genomes]
rs7615405	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628461	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7633687	0.90[EUR][1000 genomes]
rs7638204	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7643913	0.89[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	nsv822090	chr3:52292814-52311153	Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs73088783	PPM1M	cis	Artery Tibial	GTEx
rs73088783	PPM1M	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52282200-52310000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:52282400-52309600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:52282600-52308200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:52283000-52306000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:52283200-52308400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:52283400-52305400	Strong transcription	Brain Germinal Matrix	brain
7	chr3:52283600-52308800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr3:52283800-52309600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:52284600-52305800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:52285600-52308400	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:52285800-52307400	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr3:52286400-52306800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:52287400-52305400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:52287400-52305600	Strong transcription	HepG2	liver
15	chr3:52288000-52305800	Strong transcription	Fetal Muscle Leg	muscle
16	chr3:52292400-52309400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:52292800-52305800	Strong transcription	Fetal Intestine Large	intestine
18	chr3:52293000-52308000	Weak transcription	Stomach Mucosa	stomach
19	chr3:52293800-52306200	Strong transcription	NH-A	brain
20	chr3:52293800-52307200	Strong transcription	HSMM	muscle
21	chr3:52297400-52311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:52300000-52310200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:52300000-52310200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:52300200-52310200	Weak transcription	HSMMtube	muscle
25	chr3:52300600-52310800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:52301000-52305600	Weak transcription	Psoas Muscle	Psoas
27	chr3:52301200-52311400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr3:52301600-52305600	Weak transcription	Fetal Brain Male	brain
29	chr3:52301800-52307200	Genic enhancers	Adipose Nuclei	Adipose
30	chr3:52302600-52305400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:52302600-52305400	Strong transcription	Left Ventricle	heart
32	chr3:52302600-52305600	Strong transcription	Placenta	Placenta
33	chr3:52302600-52306800	Weak transcription	A549	lung
34	chr3:52302600-52307800	Weak transcription	Pancreas	Pancrea
35	chr3:52302600-52310000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr3:52302800-52305400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:52302800-52310200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:52303000-52311200	Weak transcription	Esophagus	oesophagus
39	chr3:52303400-52305800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr3:52303400-52306200	Genic enhancers	Brain Hippocampus Middle	brain
41	chr3:52303400-52310000	Weak transcription	Aorta	Aorta
42	chr3:52303600-52305600	Strong transcription	Hela-S3	cervix
43	chr3:52303600-52305800	Weak transcription	Lung	lung
44	chr3:52303600-52306200	Weak transcription	Spleen	Spleen
45	chr3:52303600-52306200	Enhancers	HUVEC	blood vessel
46	chr3:52303600-52307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:52303600-52308400	Strong transcription	NHEK	skin
48	chr3:52303600-52309600	Genic enhancers	Primary B cells from cord blood	blood
49	chr3:52303800-52306000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:52303800-52307000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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