Variant report

Variant	rs1654338
Chromosome Location	chr19:38536353-38536354
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38392598..38394693-chr19:38535463..38537612,2	MCF-7	breast:
2	chr19:38395411..38398481-chr19:38535356..38538945,3	MCF-7	breast:
3	chr19:38535066..38537554-chr19:38539866..38542740,2	MCF-7	breast:
4	chr19:38525040..38526953-chr19:38535693..38538663,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10414433	0.81[CHB][hapmap]
rs10421137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1616705	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1618385	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1620082	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1623976	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628394	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654339	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654340	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654344	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1654374	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725459	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725460	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725463	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725464	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725467	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725505	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725514	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725515	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725516	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725517	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1725518	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5022085	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5022086	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508759	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6508761	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6508762	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249241	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256480	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256626	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7256656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256804	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs734204	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106776	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs941036	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941037	0.94[AFR][1000 genomes];0.98[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:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38508600-38537000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:38514800-38537000	Weak transcription	Colonic Mucosa	Colon
3	chr19:38517000-38537000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr19:38521800-38537000	Weak transcription	Esophagus	oesophagus
5	chr19:38521800-38538400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:38521800-38538400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr19:38521800-38548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:38522000-38536600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr19:38522200-38537200	Weak transcription	Thymus	Thymus
11	chr19:38524400-38538400	Weak transcription	Small Intestine	intestine
12	chr19:38525000-38540000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr19:38525200-38536400	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr19:38525200-38536600	Weak transcription	Gastric	stomach
15	chr19:38525800-38537000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr19:38525800-38538000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr19:38526000-38537600	Weak transcription	Fetal Intestine Large	intestine
18	chr19:38526800-38545600	Weak transcription	Stomach Mucosa	stomach
19	chr19:38527800-38548800	Weak transcription	Right Atrium	heart
20	chr19:38527800-38551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
22	chr19:38528600-38538200	Weak transcription	HSMMtube	muscle
23	chr19:38528800-38543400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:38529000-38537800	Weak transcription	Fetal Muscle Leg	muscle
25	chr19:38529000-38538400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr19:38529000-38548600	Weak transcription	Pancreas	Pancrea
27	chr19:38531000-38538400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:38531400-38537200	Weak transcription	HSMM	muscle
29	chr19:38531400-38550800	Weak transcription	NHLF	lung
30	chr19:38531600-38539000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:38533800-38536600	Weak transcription	Fetal Stomach	stomach
32	chr19:38534200-38539600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr19:38534200-38540600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:38534200-38540800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:38534400-38538600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:38534400-38543200	Strong transcription	Fetal Intestine Small	intestine
37	chr19:38534600-38538200	Weak transcription	Lung	lung
38	chr19:38534600-38538600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr19:38534600-38539400	Enhancers	Primary B cells from peripheral blood	blood
40	chr19:38534800-38536400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:38534800-38536400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:38534800-38537800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:38534800-38545400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr19:38535000-38536800	Weak transcription	A549	lung
45	chr19:38535000-38538000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr19:38535200-38536800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:38535200-38540000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:38535400-38536400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr19:38535400-38536400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr19:38535400-38536800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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