Variant report

Variant	rs4774608
Chromosome Location	chr15:52431136-52431137
allele	A/G
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:7)
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	STAT3	chr15:52431107-52431288	MCF10A-Er-Src	breast:	n/a	chr15:52431230-52431241

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:52262407..52265136-chr15:52430706..52432521,2	MCF-7	breast:
2	chr15:52371129..52371827-chr15:52430855..52431660,3	MCF-7	breast:
3	chr15:52309759..52313480-chr15:52429073..52432426,3	K562	blood:
4	chr15:52418771..52421599-chr15:52429472..52431548,2	MCF-7	breast:
5	chr15:52419540..52421651-chr15:52430986..52433153,2	K562	blood:
6	chr15:52419540..52421866-chr15:52430986..52433153,3	K562	blood:
7	chr15:52312303..52314169-chr15:52430876..52432947,2	K562	blood:

No data

Variant related genes	Relation type
GNB5	TF binding region
ENSG00000069966	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11070882	0.91[ASN][1000 genomes]
rs11856177	0.91[ASN][1000 genomes]
rs12438169	0.89[EUR][1000 genomes]
rs12438190	0.86[EUR][1000 genomes]
rs12438194	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12438743	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12438937	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12440956	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12593041	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12594679	0.90[ASN][1000 genomes]
rs12595160	0.90[ASN][1000 genomes]
rs12899030	0.88[EUR][1000 genomes]
rs12899343	0.88[EUR][1000 genomes]
rs12901354	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12901730	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12901891	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12902073	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12903769	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12904831	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12904889	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12907835	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12908742	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12908833	0.91[ASN][1000 genomes]
rs12909161	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12909880	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12912428	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12916557	0.91[ASN][1000 genomes]
rs2227308	0.86[AFR][1000 genomes]
rs2398	0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34283892	0.90[ASN][1000 genomes]
rs35709612	0.89[EUR][1000 genomes]
rs35827106	0.91[ASN][1000 genomes]
rs3794540	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3794543	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4238384	0.81[ASN][1000 genomes]
rs4636859	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4638520	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4776003	0.91[ASN][1000 genomes]
rs62014721	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62014722	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8034097	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv1047647	chr15:52425879-52469181	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4774608	GNB5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
2	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
3	chr15:52410200-52441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:52410600-52441400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:52412000-52441200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:52412200-52436000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:52413600-52431800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:52416000-52432800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:52416200-52431600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:52417000-52436000	Weak transcription	Lung	lung
11	chr15:52417200-52431200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:52417200-52431800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:52417200-52436200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:52417400-52431800	Weak transcription	HMEC	breast
15	chr15:52417400-52432000	Weak transcription	NHDF-Ad	bronchial
16	chr15:52417600-52435400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:52417800-52431800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:52420400-52433600	Strong transcription	Ovary	ovary
19	chr15:52421800-52431800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr15:52422600-52431200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:52422600-52457600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:52423000-52436800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:52423000-52458200	Weak transcription	Dnd41	blood
24	chr15:52423600-52431800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:52424000-52441200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr15:52424600-52432400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:52425600-52432400	Enhancers	Liver	Liver
28	chr15:52425800-52432600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:52425800-52435400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr15:52426800-52432200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr15:52427400-52432200	Enhancers	Primary hematopoietic stem cells	blood
32	chr15:52427400-52432200	Weak transcription	Brain Angular Gyrus	brain
33	chr15:52427400-52441600	Weak transcription	Esophagus	oesophagus
34	chr15:52427600-52431200	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr15:52427800-52431800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:52427800-52432800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:52428000-52431200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:52428000-52432000	Weak transcription	Aorta	Aorta
39	chr15:52428000-52432400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr15:52428200-52431800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:52428600-52431600	Strong transcription	Hela-S3	cervix
42	chr15:52428800-52435400	Weak transcription	Osteobl	bone
43	chr15:52428800-52435800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:52428800-52440600	Weak transcription	Spleen	Spleen
45	chr15:52429000-52431400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:52429000-52446400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:52429000-52447200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr15:52429200-52431800	Weak transcription	NHLF	lung
49	chr15:52429200-52447400	Strong transcription	Primary T cells from cord blood	blood
50	chr15:52429400-52433400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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