Variant report

Variant	rs1560414
Chromosome Location	chr3:156441749-156441750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156391131..156393872-chr3:156440784..156443578,2	MCF-7	breast:
2	chr3:156440156..156442708-chr3:156446538..156448907,2	K562	blood:
3	chr3:156441208..156443920-chr3:156447407..156449224,2	K562	blood:
4	chr3:156268701..156270840-chr3:156439729..156441831,2	K562	blood:

Variant related genes	Relation type
ENSG00000243926	Chromatin interaction
ENSG00000114850	Chromatin interaction
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11709829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11917436	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13061457	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13068223	0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13095806	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13322318	0.82[JPT][hapmap]
rs13322900	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1469536	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2171542	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34111024	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34277251	0.89[ASN][1000 genomes]
rs344027	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs344035	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs345985	0.94[CHB][hapmap]
rs36126086	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3851992	0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs8792	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9868587	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156416000-156443000	Weak transcription	Aorta	Aorta
2	chr3:156422800-156442800	Weak transcription	Psoas Muscle	Psoas
3	chr3:156423000-156443200	Weak transcription	Small Intestine	intestine
4	chr3:156423000-156445800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:156424200-156443000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:156424200-156445800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:156426600-156446000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:156428600-156445200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:156429000-156443000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:156433800-156445000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:156435200-156444800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:156436200-156446200	Weak transcription	Gastric	stomach
13	chr3:156436600-156445800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:156436800-156443200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:156437000-156443000	Weak transcription	HUVEC	blood vessel
16	chr3:156437000-156446000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:156437200-156446000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:156437200-156447400	Weak transcription	Pancreas	Pancrea
19	chr3:156438800-156444400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:156439000-156447400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:156439200-156441800	Genic enhancers	Muscle Satellite Cultured Cells	--
22	chr3:156439200-156441800	Enhancers	NHDF-Ad	bronchial
23	chr3:156439400-156445800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:156439400-156446600	Enhancers	Stomach Mucosa	stomach
25	chr3:156439600-156451800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:156439800-156445800	Weak transcription	A549	lung
27	chr3:156440000-156441800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:156440200-156441800	Weak transcription	HSMM	muscle
29	chr3:156440200-156443600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:156440200-156443600	Weak transcription	Hela-S3	cervix
31	chr3:156440400-156441800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:156440400-156441800	Enhancers	NHEK	skin
33	chr3:156440400-156450200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:156440800-156442000	Strong transcription	NH-A	brain
35	chr3:156441200-156444000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr3:156441200-156445200	Weak transcription	Left Ventricle	heart
37	chr3:156441200-156445200	Weak transcription	Right Atrium	heart
38	chr3:156441200-156447400	Weak transcription	Lung	lung
39	chr3:156441400-156442600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:156441400-156442800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:156441400-156442800	Weak transcription	HMEC	breast
42	chr3:156441400-156443000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:156441400-156444000	Weak transcription	Esophagus	oesophagus
44	chr3:156441400-156445200	Weak transcription	GM12878-XiMat	blood
45	chr3:156441400-156445800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:156441400-156445800	Weak transcription	NHLF	lung
47	chr3:156441600-156442400	Strong transcription	Osteobl	bone
48	chr3:156441600-156444000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:156441600-156444600	Weak transcription	HSMMtube	muscle
50	chr3:156441600-156445800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links