Variant report

Variant	rs6783652
Chromosome Location	chr3:52323344-52323345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:52322696-52324934	HepG2	liver:	n/a	chr3:52323578-52323587
2	MYBL2	chr3:52323298-52324681	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:52322971-52323734	PBDE	blood:	n/a	n/a
4	HEY1	chr3:52323266-52324685	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:52320120-52326729	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:52322583-52323680	GM12878	blood:	n/a	n/a
7	MBD4	chr3:52323308-52324405	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52318594..52322784-chr3:52322985..52327026,4	MCF-7	breast:
2	chr3:52272181..52276088-chr3:52318615..52323958,11	MCF-7	breast:
3	chr3:52321086..52323733-chr3:52324166..52327461,5	MCF-7	breast:
4	chr3:52321755..52323526-chr3:52405745..52408434,2	K562	blood:
5	chr3:52271022..52275105-chr3:52320320..52325575,6	K562	blood:
6	chr3:52310660..52314319-chr3:52321399..52324807,9	K562	blood:
7	chr3:52321744..52323842-chr3:52332822..52334732,2	MCF-7	breast:
8	chr3:52321768..52324071-chr3:52488633..52490328,2	K562	blood:
9	chr3:52271015..52274727-chr3:52321912..52324165,4	K562	blood:

No data

Variant related genes	Relation type
WDR82	TF binding region
GLYCTK	TF binding region
ENSG00000164091	Chromatin interaction
ENSG00000247596	Chromatin interaction
ENSG00000242797	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000239557	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]
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]
rs73088791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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
rs6783652	PPM1M	cis	Artery Tibial	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52321400-52323400	Active TSS	Rectal Smooth Muscle	rectum
2	chr3:52322200-52323800	Flanking Active TSS	Liver	Liver
3	chr3:52322400-52323400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:52322400-52323800	Enhancers	Spleen	Spleen
5	chr3:52322400-52324400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:52322400-52324600	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr3:52322400-52325200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr3:52322600-52323400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:52322600-52323400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
10	chr3:52322600-52323600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:52322600-52323800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:52322600-52323800	Flanking Active TSS	Colonic Mucosa	Colon
13	chr3:52322600-52323800	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr3:52322600-52324000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:52322600-52324000	Enhancers	Fetal Intestine Large	intestine
16	chr3:52322600-52324000	Enhancers	Fetal Intestine Small	intestine
17	chr3:52322600-52324000	Flanking Active TSS	HepG2	liver
18	chr3:52322600-52324200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:52322600-52324200	Enhancers	Gastric	stomach
20	chr3:52322600-52324600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:52322600-52324600	Enhancers	Pancreas	Pancrea
22	chr3:52322600-52324800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:52322600-52325200	Weak transcription	Ovary	ovary
24	chr3:52322600-52325400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr3:52322600-52331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:52322600-52332000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:52322600-52334400	Weak transcription	NHDF-Ad	bronchial
28	chr3:52322800-52323400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr3:52322800-52323400	Enhancers	Primary T cells from cord blood	blood
30	chr3:52322800-52323400	Enhancers	Primary hematopoietic stem cells	blood
31	chr3:52322800-52323400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr3:52322800-52323400	Enhancers	Brain Angular Gyrus	brain
33	chr3:52322800-52323400	Enhancers	Colon Smooth Muscle	Colon
34	chr3:52322800-52323400	Weak transcription	Right Ventricle	heart
35	chr3:52322800-52323400	Enhancers	Thymus	Thymus
36	chr3:52322800-52323400	Enhancers	HUVEC	blood vessel
37	chr3:52322800-52323600	Enhancers	Primary B cells from peripheral blood	blood
38	chr3:52322800-52323600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:52322800-52323600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr3:52322800-52323600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr3:52322800-52323600	Enhancers	HSMM	muscle
42	chr3:52322800-52323800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr3:52322800-52324000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:52322800-52324400	Enhancers	Placenta	Placenta
45	chr3:52322800-52324600	Enhancers	Primary T cells fromperipheralblood	blood
46	chr3:52322800-52324600	Weak transcription	Esophagus	oesophagus
47	chr3:52322800-52324800	Enhancers	A549	lung
48	chr3:52322800-52325000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:52322800-52325800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:52322800-52326400	Weak transcription	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links