Variant report

Variant	rs1473116
Chromosome Location	chr19:18782197-18782198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18367818..18369812-chr19:18780764..18782671,2	K562	blood:
2	chr19:18781923..18783867-chr19:18787837..18789720,2	K562	blood:
3	chr19:18781390..18783867-chr19:18783988..18789720,5	K562	blood:
4	chr19:18781801..18783943-chr19:18794060..18796005,2	MCF-7	breast:
5	chr19:18758073..18760878-chr19:18781482..18783635,2	K562	blood:
6	chr19:18771428..18776633-chr19:18776726..18782954,6	K562	blood:
7	chr19:18777346..18780896-chr19:18782148..18785214,5	K562	blood:

Variant related genes	Relation type
ENSG00000105662	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10221489	0.85[CHB][hapmap]
rs10412053	0.94[ASN][1000 genomes]
rs10412858	0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[ASN][1000 genomes]
rs10419226	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10420228	0.91[ASN][1000 genomes]
rs10421503	1.00[ASN][1000 genomes]
rs10423674	0.85[CHB][hapmap]
rs10424265	0.82[ASN][1000 genomes]
rs10854003	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[ASN][1000 genomes]
rs11085236	0.91[ASN][1000 genomes]
rs11883401	0.96[ASN][1000 genomes]
rs12976113	0.97[ASN][1000 genomes]
rs2214524	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2385178	0.90[ASN][1000 genomes]
rs2891698	0.82[ASN][1000 genomes]
rs3829671	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4808145	0.90[ASN][1000 genomes]
rs4808147	0.95[ASN][1000 genomes]
rs6510995	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6510996	0.96[ASN][1000 genomes]
rs7246437	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[ASN][1000 genomes]
rs7257812	0.98[ASN][1000 genomes]
rs757347	0.94[ASN][1000 genomes]
rs8100824	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[ASN][1000 genomes]
rs8102046	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs876982	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[ASN][1000 genomes]
rs886443	0.98[ASN][1000 genomes]
rs889364	0.91[ASN][1000 genomes]

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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1473116	GDF1	cis	parietal	SCAN
rs1473116	UBA52	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18760400-18794800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:18770400-18793600	Weak transcription	GM12878-XiMat	blood
3	chr19:18770800-18783200	Weak transcription	Stomach Mucosa	stomach
4	chr19:18771600-18783400	Weak transcription	HUVEC	blood vessel
5	chr19:18771800-18788200	Weak transcription	K562	blood
6	chr19:18773200-18788000	Weak transcription	NHEK	skin
7	chr19:18774200-18783400	Weak transcription	A549	lung
8	chr19:18774400-18784000	Strong transcription	Fetal Intestine Small	intestine
9	chr19:18774600-18783800	Weak transcription	HepG2	liver
10	chr19:18774600-18787400	Weak transcription	Hela-S3	cervix
11	chr19:18774800-18783000	Weak transcription	HSMM	muscle
12	chr19:18774800-18788000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:18775000-18783000	Strong transcription	Brain Germinal Matrix	brain
14	chr19:18775000-18783200	Strong transcription	Fetal Brain Female	brain
15	chr19:18775200-18793800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:18775400-18782800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:18775400-18783000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:18775600-18783400	Strong transcription	Dnd41	blood
19	chr19:18776000-18782400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:18776000-18783200	Strong transcription	Spleen	Spleen
21	chr19:18776000-18783600	Strong transcription	Thymus	Thymus
22	chr19:18776200-18782200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:18776200-18783400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:18776800-18783000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:18777400-18782800	Weak transcription	Psoas Muscle	Psoas
26	chr19:18777800-18782600	Weak transcription	Right Atrium	heart
27	chr19:18777800-18793800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr19:18778000-18782200	Strong transcription	Fetal Stomach	stomach
29	chr19:18778400-18782200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:18778400-18783400	Strong transcription	Primary T cells from cord blood	blood
31	chr19:18778600-18782800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr19:18779200-18782800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr19:18779400-18782600	Strong transcription	Lung	lung
34	chr19:18779800-18782400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:18779800-18783400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr19:18780000-18782400	Weak transcription	Fetal Lung	lung
37	chr19:18780000-18785000	Weak transcription	Brain Angular Gyrus	brain
38	chr19:18780000-18788200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr19:18780000-18788800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr19:18780200-18782200	Weak transcription	Placenta	Placenta
41	chr19:18780200-18782400	Weak transcription	NHLF	lung
42	chr19:18780200-18782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:18780200-18783200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:18780200-18784000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr19:18780200-18786800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:18780200-18788000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:18780200-18788000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:18780200-18788800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr19:18780200-18793400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr19:18780200-18793800	Weak transcription	H9 Cell Line	embryonic stem cell

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