Variant report

Variant	rs3787082
Chromosome Location	chr20:25235736-25235737
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25203986..25207347-chr20:25234571..25237258,3	MCF-7	breast:
2	chr20:25175542..25177636-chr20:25234682..25237222,2	MCF-7	breast:
3	chr20:25213915..25215962-chr20:25232689..25235985,3	MCF-7	breast:
4	chr20:25232688..25236951-chr20:25237254..25241133,6	K562	blood:
5	chr20:25233973..25236951-chr20:25237621..25241133,4	K562	blood:
6	chr20:25175034..25178574-chr20:25233747..25236675,3	MCF-7	breast:
7	chr20:25214183..25215776-chr20:25234769..25237160,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197586	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1555329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555330	0.80[EUR][1000 genomes]
rs2257649	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2259961	0.82[EUR][1000 genomes]
rs2424703	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474764	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2474765	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474780	0.82[EUR][1000 genomes]
rs2500413	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2500430	0.80[EUR][1000 genomes]
rs2983489	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815400	0.82[EUR][1000 genomes]
rs6050498	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107017	0.80[EUR][1000 genomes]
rs6107027	0.82[EUR][1000 genomes]
rs6115107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132821	0.80[EUR][1000 genomes]
rs6132824	0.80[EUR][1000 genomes]
rs6132825	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8184820	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer 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 target site	53 gene(s)	inside rSNPs	diseases
7	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
12	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
13	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
18	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3787082	GINS1	Cis_1M	lymphoblastoid	RTeQTL
rs3787082	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs3787082	PYGB	cis	multi-tissue	Pritchard
rs3787082	ABHD12	cis	Artery Tibial	GTEx
rs3787082	ABHD12	cis	multi-tissue	Pritchard
rs3787082	PYGB	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25229800-25250000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr20:25230200-25235800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr20:25230200-25236000	Weak transcription	Psoas Muscle	Psoas
4	chr20:25230200-25237400	Weak transcription	Fetal Thymus	thymus
5	chr20:25230200-25239000	Weak transcription	Primary B cells from cord blood	blood
6	chr20:25230200-25239600	Enhancers	Stomach Mucosa	stomach
7	chr20:25230200-25239800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr20:25230200-25240400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr20:25230200-25240400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr20:25230400-25239800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr20:25230400-25239800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr20:25230400-25291600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr20:25230600-25239800	Weak transcription	Fetal Lung	lung
14	chr20:25231000-25239400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr20:25231000-25239800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr20:25231000-25240400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr20:25231200-25237200	Weak transcription	Ovary	ovary
18	chr20:25231200-25239200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr20:25231200-25251800	Weak transcription	Hela-S3	cervix
20	chr20:25231200-25252200	Weak transcription	HUVEC	blood vessel
21	chr20:25231400-25235800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr20:25231400-25236400	Enhancers	Brain Hippocampus Middle	brain
23	chr20:25231400-25240000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr20:25231400-25240800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr20:25231400-25249800	Weak transcription	Small Intestine	intestine
26	chr20:25231800-25237200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr20:25231800-25237200	Weak transcription	NHDF-Ad	bronchial
28	chr20:25232000-25235800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr20:25232000-25237400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr20:25232000-25239400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr20:25232000-25239400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr20:25232200-25236000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr20:25232200-25238200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr20:25232400-25236000	Weak transcription	HSMMtube	muscle
35	chr20:25232400-25237200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr20:25232400-25237600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:25232600-25238600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr20:25232600-25240000	Weak transcription	Thymus	Thymus
39	chr20:25233000-25236000	Genic enhancers	Osteobl	bone
40	chr20:25233000-25236200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr20:25233200-25235800	Weak transcription	Aorta	Aorta
42	chr20:25233200-25235800	Weak transcription	Colonic Mucosa	Colon
43	chr20:25233200-25236000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr20:25233200-25238400	Weak transcription	K562	blood
45	chr20:25233200-25239200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr20:25233200-25239400	Enhancers	Primary T cells from cord blood	blood
47	chr20:25233200-25252200	Weak transcription	Fetal Brain Male	brain
48	chr20:25233400-25235800	Weak transcription	NHLF	lung
49	chr20:25233400-25236200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr20:25233400-25236600	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links