Variant report

Variant	rs3852062
Chromosome Location	chr3:52267885-52267886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr3:52267817-52268148	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52254403..52255299-chr3:52267830..52268524,2	MCF-7	breast:
2	chr3:52263321..52268061-chr3:52310039..52314728,5	K562	blood:
3	chr3:52264729..52268939-chr3:52269297..52274565,7	K562	blood:
4	chr3:52266609..52268371-chr3:52308578..52311025,2	MCF-7	breast:
5	chr3:52262375..52268246-chr3:52270366..52274345,8	K562	blood:
6	chr3:52237538..52239205-chr3:52267167..52269344,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173366	TF binding region
TWF2	TF binding region
ENSG00000247596	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000239732	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11706541	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11711914	0.82[AMR][1000 genomes]
rs11713464	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11714313	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714358	0.82[AMR][1000 genomes]
rs11717574	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718729	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11719760	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17052051	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17052053	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1767	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1769	0.82[AMR][1000 genomes]
rs3733063	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs55847657	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56352611	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5743836	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58531656	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58879205	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60382084	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61644644	0.82[AMR][1000 genomes]
rs61729402	0.87[ASN][1000 genomes]
rs61729450	0.87[ASN][1000 genomes]
rs67767125	0.94[EUR][1000 genomes]
rs6793317	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6809248	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73088773	0.82[AMR][1000 genomes]
rs73088783	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73088785	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73088800	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7643913	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	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
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3852062	PPM1M	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52247800-52272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:52253200-52269600	Weak transcription	Fetal Kidney	kidney
3	chr3:52255000-52268600	Weak transcription	Right Atrium	heart
4	chr3:52255200-52270400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:52259600-52268200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:52261000-52269400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:52261200-52270800	Strong transcription	Fetal Stomach	stomach
8	chr3:52261400-52269000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:52261400-52269600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:52261600-52269800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:52261600-52270000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:52261600-52270000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:52261600-52270600	Strong transcription	NHEK	skin
14	chr3:52261800-52269400	Strong transcription	Brain Germinal Matrix	brain
15	chr3:52261800-52269800	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr3:52261800-52269800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:52261800-52270000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:52261800-52270800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:52262000-52269200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:52262400-52269800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:52262400-52269800	Strong transcription	Osteobl	bone
22	chr3:52262400-52270000	Strong transcription	NHLF	lung
23	chr3:52262800-52268600	Strong transcription	Ovary	ovary
24	chr3:52263000-52269800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:52263200-52269000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:52264200-52271400	Genic enhancers	Primary T cells fromperipheralblood	blood
27	chr3:52264600-52270000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr3:52264800-52270600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:52265000-52269400	Weak transcription	Hela-S3	cervix
30	chr3:52265000-52270400	Weak transcription	K562	blood
31	chr3:52265000-52272000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:52265200-52269400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr3:52265200-52270400	Weak transcription	HSMMtube	muscle
34	chr3:52265200-52270800	Weak transcription	HUVEC	blood vessel
35	chr3:52265400-52269200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:52265400-52269200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:52265400-52269600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr3:52265400-52269800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr3:52265400-52270800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr3:52265400-52271800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:52265600-52268600	Weak transcription	A549	lung
42	chr3:52265600-52269600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:52265600-52270400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:52265600-52270400	Weak transcription	Brain Substantia Nigra	brain
45	chr3:52265600-52270400	Strong transcription	Fetal Intestine Small	intestine
46	chr3:52265600-52270400	Weak transcription	Stomach Mucosa	stomach
47	chr3:52265600-52270400	Weak transcription	HMEC	breast
48	chr3:52265600-52270600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:52265600-52270600	Weak transcription	Small Intestine	intestine
50	chr3:52265600-52270800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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