Variant report

Variant	rs1057745
Chromosome Location	chr19:39888390-39888391
allele	C/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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39887960..39888930-chr19:39901705..39903106,10	MCF-7	breast:
2	chr19:39887250..39889651-chr19:39901829..39904000,29	K562	blood:
3	chr19:39888340..39888931-chr19:40030782..40031358,2	K562	blood:
4	chr19:39879787..39883867-chr19:39884525..39889123,13	K562	blood:
5	chr19:39888112..39888670-chr19:39900140..39900761,2	MCF-7	breast:
6	chr19:39887866..39890343-chr19:40030809..40032954,2	MCF-7	breast:
7	chr19:39888121..39888928-chr19:39903340..39903937,3	MCF-7	breast:
8	chr19:39887994..39889005-chr19:39901768..39903114,14	MCF-7	breast:
9	chr19:39888249..39888993-chr19:39900394..39901778,4	K562	blood:
10	chr19:39832883..39834825-chr19:39888333..39890047,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130755	Chromatin interaction
ENSG00000006712	Chromatin interaction
ENSG00000266559	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000090924	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12459135	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56138629	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58587357	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250234	0.89[YRI][hapmap]
rs8102889	0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1057745	CEACAM7	cis	cerebellum	SCAN
rs1057745	CXCL17	cis	cerebellum	SCAN
rs1057745	DKFZp434H247	cis	multi-tissue	Pritchard
rs1057745	ZNF780A	cis	parietal	SCAN
rs1057745	ENSG00000063322	cis	multi-tissue	Pritchard
rs1057745	IXL	cis	multi-tissue	Pritchard
rs1057745	MED29	cis	lymphoblastoid	seeQTL
rs1057745	TGFB1	cis	cerebellum	SCAN
rs1057745	MED29	cis	Lymphoblastoid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39883000-39888600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:39883000-39888600	Weak transcription	Small Intestine	intestine
3	chr19:39883000-39891800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:39883200-39888600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:39883200-39891600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:39883200-39892400	Weak transcription	Fetal Brain Male	brain
7	chr19:39883200-39892400	Weak transcription	Fetal Kidney	kidney
8	chr19:39884200-39889600	Strong transcription	Brain Germinal Matrix	brain
9	chr19:39884600-39888400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:39884800-39888600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:39885000-39892600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:39885400-39888600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:39886200-39888600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr19:39886200-39888600	Weak transcription	Osteobl	bone
15	chr19:39886200-39892000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:39886200-39892400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr19:39886800-39893400	Weak transcription	Aorta	Aorta
18	chr19:39886800-39893400	Weak transcription	Ovary	ovary
19	chr19:39887000-39888400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:39887200-39888400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:39887200-39888800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:39887600-39888400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr19:39887600-39888600	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr19:39887600-39888600	Genic enhancers	Colonic Mucosa	Colon
25	chr19:39887800-39888400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr19:39887800-39888400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr19:39887800-39888400	Flanking Active TSS	Liver	Liver
28	chr19:39887800-39888400	Genic enhancers	Duodenum Mucosa	Duodenum
29	chr19:39887800-39888400	Genic enhancers	Rectal Mucosa Donor 31	rectum
30	chr19:39887800-39888400	Genic enhancers	Stomach Smooth Muscle	stomach
31	chr19:39887800-39888400	Genic enhancers	GM12878-XiMat	blood
32	chr19:39887800-39888600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr19:39887800-39888600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:39887800-39888600	Genic enhancers	A549	lung
35	chr19:39887800-39888600	Enhancers	HepG2	liver
36	chr19:39887800-39888600	Genic enhancers	HSMM	muscle
37	chr19:39887800-39888800	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr19:39887800-39888800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:39887800-39888800	Genic enhancers	Colon Smooth Muscle	Colon
40	chr19:39887800-39889000	Genic enhancers	Brain Hippocampus Middle	brain
41	chr19:39887800-39889600	Genic enhancers	Pancreas	Pancrea
42	chr19:39887800-39889600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
43	chr19:39887800-39889600	Genic enhancers	Spleen	Spleen
44	chr19:39887800-39889800	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:39887800-39889800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr19:39887800-39890600	Genic enhancers	Fetal Thymus	thymus
47	chr19:39888000-39888400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr19:39888000-39888400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
49	chr19:39888000-39888400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr19:39888000-39888400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links