Variant report

Variant	rs2189517
Chromosome Location	chr14:69002988-69002989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:69001801..69004663-chr14:69006865..69008433,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10134446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1023529	0.88[JPT][hapmap]
rs1023530	0.81[CHB][hapmap]
rs11158749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12587232	0.80[TSI][hapmap]
rs12882030	0.81[CHB][hapmap]
rs12887124	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476586	0.88[JPT][hapmap]
rs1859302	0.88[JPT][hapmap]
rs2078316	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs2158358	0.88[JPT][hapmap]
rs2247048	0.88[JPT][hapmap]
rs2525521	0.88[JPT][hapmap]
rs2525523	0.87[JPT][hapmap]
rs2525524	0.88[JPT][hapmap]
rs2525525	0.88[JPT][hapmap]
rs2525526	0.88[JPT][hapmap]
rs2525527	0.81[JPT][hapmap]
rs2525530	0.92[CEU][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2679	0.90[CHB][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs2842329	0.81[JPT][hapmap]
rs2842331	0.87[JPT][hapmap]
rs7140266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs916962	0.94[JPT][hapmap]
rs9323513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9323514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[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	nsv869154	chr14:68366754-69041768	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv832822	chr14:68874640-69060272	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1048064	chr14:68991041-69012766	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2189517	SIPA1L1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:68996200-69007800	Weak transcription	Stomach Mucosa	stomach
2	chr14:69000000-69003000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr14:69001200-69003600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr14:69001200-69003600	Enhancers	HMEC	breast
5	chr14:69001800-69003000	Enhancers	Hela-S3	cervix
6	chr14:69001800-69003000	Enhancers	HSMM	muscle
7	chr14:69001800-69003200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr14:69001800-69003200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr14:69001800-69003200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr14:69001800-69003400	Enhancers	NHLF	lung
11	chr14:69001800-69003600	Enhancers	NHEK	skin
12	chr14:69002000-69003000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:69002000-69003200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr14:69002000-69003600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr14:69002200-69003000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr14:69002200-69003000	Enhancers	HSMMtube	muscle
17	chr14:69002200-69003200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr14:69002200-69003200	Enhancers	Osteobl	bone
19	chr14:69002400-69003200	Enhancers	NH-A	brain
20	chr14:69002400-69016600	Weak transcription	Gastric	stomach
21	chr14:69002600-69003000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr14:69002600-69004800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:69002600-69006600	Weak transcription	Ovary	ovary
24	chr14:69002800-69003000	Enhancers	Fetal Muscle Leg	muscle
25	chr14:69002800-69003000	Enhancers	Psoas Muscle	Psoas
26	chr14:69002800-69003400	Enhancers	NHDF-Ad	bronchial
27	chr14:69002800-69005600	Weak transcription	A549	lung
28	chr14:69002800-69006000	Weak transcription	Esophagus	oesophagus
29	chr14:69002800-69006000	Weak transcription	Placenta	Placenta
30	chr14:69002800-69006200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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