Variant report

Variant	rs1725458
Chromosome Location	chr19:38539639-38539640
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38536919..38539857-chr19:38546336..38549033,2	MCF-7	breast:
2	chr19:38440998..38442982-chr19:38537686..38540589,2	MCF-7	breast:
3	chr19:38537912..38540463-chr19:38546396..38548192,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10413751	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10414433	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1612361	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1654341	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1654343	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1654347	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1654349	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1654350	0.91[EUR][1000 genomes]
rs1654352	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1725462	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1725470	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1725475	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1725476	0.92[EUR][1000 genomes]
rs1725506	0.81[EUR][1000 genomes]
rs1725507	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1725508	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1725509	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1725510	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28587798	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57585457	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57999412	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7257303	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs734365	0.94[ASN][1000 genomes]
rs855597	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs855598	0.81[EUR][1000 genomes]
rs855599	0.81[EUR][1000 genomes]
rs855600	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs855601	0.84[EUR][1000 genomes]
rs855605	0.94[ASN][1000 genomes]
rs855636	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs855637	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv911656	chr19:38505037-38539988	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1060359	chr19:38512719-38552438	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1725458	DPF1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38521800-38548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:38525000-38540000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr19:38526800-38545600	Weak transcription	Stomach Mucosa	stomach
5	chr19:38527800-38548800	Weak transcription	Right Atrium	heart
6	chr19:38527800-38551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
8	chr19:38528800-38543400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr19:38529000-38548600	Weak transcription	Pancreas	Pancrea
10	chr19:38531400-38550800	Weak transcription	NHLF	lung
11	chr19:38534200-38540600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:38534200-38540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:38534400-38543200	Strong transcription	Fetal Intestine Small	intestine
14	chr19:38534800-38545400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:38535200-38540000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:38536000-38540800	Enhancers	Primary hematopoietic stem cells	blood
17	chr19:38536200-38540800	Enhancers	Fetal Thymus	thymus
18	chr19:38536200-38543400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr19:38537200-38539800	Enhancers	Thymus	Thymus
20	chr19:38537800-38540400	Enhancers	Fetal Muscle Leg	muscle
21	chr19:38537800-38545400	Weak transcription	Fetal Stomach	stomach
22	chr19:38537800-38548800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:38537800-38548800	Weak transcription	Esophagus	oesophagus
24	chr19:38538000-38540000	Enhancers	Duodenum Mucosa	Duodenum
25	chr19:38538000-38548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:38538200-38540000	Enhancers	Fetal Muscle Trunk	muscle
27	chr19:38538200-38540200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr19:38538400-38540000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:38538400-38540200	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr19:38538400-38540200	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr19:38538400-38543400	Weak transcription	Fetal Intestine Large	intestine
32	chr19:38538400-38552800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:38538600-38539800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:38538600-38540000	Weak transcription	Lung	lung
35	chr19:38538600-38540400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
36	chr19:38538600-38540400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr19:38538600-38543200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:38538800-38539800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:38538800-38540400	Flanking Active TSS	Dnd41	blood
40	chr19:38538800-38540600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr19:38538800-38540600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr19:38539000-38539800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:38539000-38539800	Enhancers	Osteobl	bone
44	chr19:38539000-38540000	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr19:38539000-38545200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:38539000-38545400	Weak transcription	Gastric	stomach
47	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
48	chr19:38539200-38539800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:38539200-38539800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:38539200-38540000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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