Variant report

Variant	rs754245
Chromosome Location	chr19:18760567-18760568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18757758..18761197-chr19:18765478..18769110,5	MCF-7	breast:
2	chr19:18758073..18760878-chr19:18781482..18783635,2	K562	blood:
3	chr19:18716960..18718504-chr19:18758671..18760840,2	MCF-7	breast:
4	chr19:18754096..18756985-chr19:18760445..18762017,2	MCF-7	breast:
5	chr19:18722195..18724097-chr19:18759518..18761356,2	K562	blood:
6	chr19:18752753..18754292-chr19:18759616..18761597,2	K562	blood:
7	chr19:18759533..18761540-chr19:18773488..18775282,2	K562	blood:
8	chr19:18759439..18761865-chr19:18767134..18771094,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000167487	Chromatin interaction
ENSG00000006016	Chromatin interaction
ENSG00000105696	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13344627	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1862646	1.00[ASN][1000 genomes]
rs28793742	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3795027	0.81[GIH][hapmap]
rs59186604	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59333602	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73923135	0.91[ASN][1000 genomes]
rs8107586	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	esv1849639	chr19:18747006-18780799	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs754245	MAST3	cis	cerebellum	SCAN
rs754245	GDF1	cis	parietal	SCAN
rs754245	MYO9B	cis	cerebellum	SCAN
rs754245	BRD4	cis	cerebellum	SCAN
rs754245	PGLS	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18748400-18761600	Weak transcription	Aorta	Aorta
2	chr19:18748600-18774400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:18749200-18768200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:18749200-18778400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:18749400-18762200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr19:18749400-18774000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr19:18749800-18760800	Weak transcription	Dnd41	blood
8	chr19:18755600-18762200	Weak transcription	NHEK	skin
9	chr19:18755800-18764000	Enhancers	Right Ventricle	heart
10	chr19:18755800-18766600	Weak transcription	HepG2	liver
11	chr19:18756400-18778400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:18757400-18762000	Enhancers	Fetal Kidney	kidney
13	chr19:18758000-18762800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:18758400-18762600	Enhancers	Fetal Heart	heart
15	chr19:18758800-18762200	Weak transcription	K562	blood
16	chr19:18758800-18762800	Genic enhancers	Fetal Stomach	stomach
17	chr19:18758800-18763000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr19:18758800-18763000	Enhancers	Placenta	Placenta
19	chr19:18759000-18761600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:18759200-18761000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr19:18759200-18761200	Enhancers	Primary B cells from peripheral blood	blood
22	chr19:18759200-18761200	Enhancers	Psoas Muscle	Psoas
23	chr19:18759200-18761200	Enhancers	NH-A	brain
24	chr19:18759200-18762200	Genic enhancers	Spleen	Spleen
25	chr19:18759200-18762600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr19:18759200-18763000	Enhancers	Fetal Thymus	thymus
27	chr19:18759400-18760800	Enhancers	Primary T cells fromperipheralblood	blood
28	chr19:18759400-18761000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:18759400-18761000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr19:18759400-18761000	Enhancers	GM12878-XiMat	blood
31	chr19:18759400-18761200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr19:18759400-18761200	Enhancers	Fetal Intestine Large	intestine
33	chr19:18759400-18761400	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr19:18759400-18761600	Genic enhancers	Fetal Intestine Small	intestine
35	chr19:18759400-18762000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr19:18759400-18762200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:18759400-18762600	Enhancers	HUVEC	blood vessel
38	chr19:18759400-18762800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:18759400-18762800	Enhancers	Lung	lung
40	chr19:18759400-18776200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:18759600-18760600	Enhancers	Osteobl	bone
42	chr19:18759600-18760800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr19:18759600-18760800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr19:18759600-18760800	Enhancers	Liver	Liver
45	chr19:18759600-18760800	Enhancers	Ovary	ovary
46	chr19:18759600-18761200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr19:18759600-18762000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr19:18759600-18762400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:18759600-18763200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:18759800-18760800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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