Variant report

Variant	rs7615405
Chromosome Location	chr3:52351553-52351554
allele	G/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	JUND	chr3:52351391-52351905	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3AK20	chr3:52351551-52352016	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD2	chr3:52351514-52351911	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:52351552-52351891	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:52351515-52351975	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3A	chr3:52351330-52352080	H1-hESC	embryonic stem cell:	n/a	n/a
7	ELF1	chr3:52351520-52352056	GM12878	blood:	n/a	n/a
8	MTA3	chr3:52351259-52351917	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:52351553-52351845	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52347614..52350493-chr3:52351552..52354517,2	K562	blood:

Variant related genes	Relation type
DNAH1	TF binding region
ENSG00000114841	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10460962	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10461027	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10461028	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10865971	0.85[EUR][1000 genomes]
rs11706515	0.97[EUR][1000 genomes]
rs11706541	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11707056	0.97[EUR][1000 genomes]
rs11707931	0.87[AFR][1000 genomes]
rs11708581	0.97[EUR][1000 genomes]
rs11708811	0.97[EUR][1000 genomes]
rs11710014	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11711914	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11711934	0.88[AFR][1000 genomes]
rs11711974	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11713464	0.81[AMR][1000 genomes]
rs11713914	0.97[EUR][1000 genomes]
rs11714358	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11715208	0.97[EUR][1000 genomes]
rs11715382	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11715391	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11716487	0.81[EUR][1000 genomes]
rs11717028	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11718729	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11719760	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11720365	0.97[EUR][1000 genomes]
rs11721277	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13059674	0.89[AFR][1000 genomes]
rs17052051	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052052	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052053	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17052054	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17052058	0.89[AFR][1000 genomes]
rs17052061	0.89[AFR][1000 genomes]
rs17052068	0.89[AFR][1000 genomes]
rs17263770	0.84[EUR][1000 genomes]
rs1767	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1769	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2335640	0.86[AFR][1000 genomes]
rs34238085	0.89[AFR][1000 genomes]
rs34523877	0.89[AFR][1000 genomes]
rs34762015	0.87[AFR][1000 genomes]
rs35133416	0.87[AFR][1000 genomes]
rs35976326	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3733063	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3886875	0.91[EUR][1000 genomes]
rs4082828	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55676974	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55806905	0.97[EUR][1000 genomes]
rs55813842	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55847657	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55965068	0.88[AFR][1000 genomes]
rs55997317	0.89[AFR][1000 genomes]
rs56002041	0.97[EUR][1000 genomes]
rs56322342	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56352611	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56357549	0.89[AFR][1000 genomes]
rs56899118	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57441156	0.93[AFR][1000 genomes]
rs57849650	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58531656	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58879205	0.81[AMR][1000 genomes]
rs60382084	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61150019	0.89[AFR][1000 genomes]
rs61644644	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6445385	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6445386	0.89[AFR][1000 genomes]
rs6763882	0.86[AFR][1000 genomes]
rs6776759	0.84[EUR][1000 genomes]
rs6783652	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6793317	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6796333	0.88[AFR][1000 genomes]
rs6809248	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs724801	0.85[EUR][1000 genomes]
rs729555	0.85[EUR][1000 genomes]
rs73072990	0.91[EUR][1000 genomes]
rs73088773	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088783	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73088785	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73088791	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73088800	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73091166	0.97[EUR][1000 genomes]
rs73091168	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs746239	0.97[EUR][1000 genomes]
rs7628461	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7633687	0.97[EUR][1000 genomes]
rs7638204	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7643913	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	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
7	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
rs7615405	PPM1M	cis	Artery Tibial	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52327200-52351600	Weak transcription	Aorta	Aorta
2	chr3:52327400-52351600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:52328200-52366000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:52328800-52367600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:52329200-52351600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:52330400-52378600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:52333000-52351600	Weak transcription	Thymus	Thymus
8	chr3:52344600-52378600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:52345800-52351600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:52345800-52351600	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:52348000-52351600	Weak transcription	NHLF	lung
12	chr3:52348000-52353600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:52348400-52351600	Weak transcription	Stomach Mucosa	stomach
14	chr3:52348800-52351600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:52349000-52351600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:52349000-52351600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:52349000-52351600	Weak transcription	NHDF-Ad	bronchial
18	chr3:52349000-52357200	Weak transcription	HepG2	liver
19	chr3:52349400-52351600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:52350200-52351600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:52350200-52351600	Weak transcription	HSMM	muscle
22	chr3:52350600-52353800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:52350600-52362400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:52351000-52351600	Enhancers	Brain Germinal Matrix	brain
25	chr3:52351000-52351600	Enhancers	Fetal Brain Male	brain
26	chr3:52351000-52352000	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr3:52351000-52353600	Weak transcription	Liver	Liver
28	chr3:52351200-52351600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
29	chr3:52351200-52351600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:52351200-52351600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:52351200-52351600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:52351200-52351600	Enhancers	Primary B cells from peripheral blood	blood
33	chr3:52351200-52351600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr3:52351200-52351600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:52351200-52351600	Enhancers	Esophagus	oesophagus
36	chr3:52351200-52351600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr3:52351200-52351600	Enhancers	Fetal Thymus	thymus
38	chr3:52351200-52351600	Enhancers	Left Ventricle	heart
39	chr3:52351200-52351600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:52351200-52351800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:52351200-52351800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr3:52351200-52351800	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr3:52351200-52351800	Active TSS	Pancreas	Pancrea
44	chr3:52351200-52351800	Flanking Active TSS	Osteobl	bone
45	chr3:52351200-52352000	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr3:52351200-52352000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:52351200-52352000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:52351200-52352000	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr3:52351200-52352000	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr3:52351200-52352000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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