Variant report

Variant	rs1654339
Chromosome Location	chr19:38538799-38538800
allele	A/G
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	chr19:38395411..38398481-chr19:38535356..38538945,3	MCF-7	breast:
3	chr19:38440998..38442982-chr19:38537686..38540589,2	MCF-7	breast:
4	chr19:38537912..38540463-chr19:38546396..38548192,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10421137	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1616705	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1618385	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1620082	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1623976	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628394	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654338	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654340	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654344	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1654374	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725459	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725463	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725464	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725467	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725505	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725514	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725515	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725516	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725517	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725518	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5022085	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5022086	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508759	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6508761	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508762	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249241	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256480	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256626	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256656	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256804	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs734204	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106776	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs941036	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941037	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][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

No data

Chromatin state (count:90 , 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	chr19:38531600-38539000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:38534200-38539600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr19:38534200-38540600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:38534200-38540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:38534400-38543200	Strong transcription	Fetal Intestine Small	intestine
16	chr19:38534600-38539400	Enhancers	Primary B cells from peripheral blood	blood
17	chr19:38534800-38545400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:38535200-38540000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:38535400-38538800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr19:38535400-38539400	Enhancers	Primary B cells from cord blood	blood
21	chr19:38535800-38539200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:38536000-38539200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr19:38536000-38539200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:38536000-38540800	Enhancers	Primary hematopoietic stem cells	blood
25	chr19:38536200-38539200	Enhancers	Primary T cells fromperipheralblood	blood
26	chr19:38536200-38539400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:38536200-38539400	Flanking Active TSS	GM12878-XiMat	blood
28	chr19:38536200-38540800	Enhancers	Fetal Thymus	thymus
29	chr19:38536200-38543400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:38536400-38538800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr19:38536400-38539000	Enhancers	Primary T cells from cord blood	blood
32	chr19:38536400-38539400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr19:38536600-38538800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr19:38536600-38539000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr19:38536800-38538800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr19:38536800-38539200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:38536800-38539400	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr19:38537000-38539200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:38537200-38538800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:38537200-38539400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:38537200-38539800	Enhancers	Thymus	Thymus
42	chr19:38537400-38538800	Enhancers	Dnd41	blood
43	chr19:38537600-38539200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr19:38537600-38539400	Enhancers	NH-A	brain
45	chr19:38537800-38539000	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr19:38537800-38539000	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr19:38537800-38539200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:38537800-38539400	Enhancers	Spleen	Spleen
49	chr19:38537800-38540400	Enhancers	Fetal Muscle Leg	muscle
50	chr19:38537800-38545400	Weak transcription	Fetal Stomach	stomach

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