Variant report

Variant	rs1488371
Chromosome Location	chr3:45938089-45938090
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:45932573..45935155-chr3:45936845..45938513,2	MCF-7	breast:
2	chr3:45936711..45939307-chr3:45956614..45959025,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163818	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1860264	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1985356	0.82[ASN][1000 genomes]
rs2286486	0.81[CHD][hapmap]
rs28501674	0.83[ASN][1000 genomes]
rs34549672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34847985	0.81[ASN][1000 genomes]
rs4683147	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs57295094	0.83[ASN][1000 genomes]
rs57527954	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61565453	0.83[ASN][1000 genomes]
rs62245098	0.83[ASN][1000 genomes]
rs62245102	0.82[ASN][1000 genomes]
rs6441929	0.81[CHD][hapmap]
rs6441930	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6441932	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441933	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6791859	0.82[ASN][1000 genomes]
rs6798047	0.89[ASN][1000 genomes]
rs7613548	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7614342	0.82[ASN][1000 genomes]
rs875890	0.83[ASN][1000 genomes]
rs875891	0.83[ASN][1000 genomes]
rs9834860	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9852270	0.92[CEU][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9862611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9868455	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1488371	CDC25A	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45923400-45948200	Weak transcription	Right Atrium	heart
2	chr3:45925200-45949600	Weak transcription	Pancreas	Pancrea
3	chr3:45925600-45947800	Genic enhancers	Dnd41	blood
4	chr3:45932400-45960200	Weak transcription	Fetal Intestine Small	intestine
5	chr3:45934000-45960200	Weak transcription	Right Ventricle	heart
6	chr3:45934200-45938400	Weak transcription	Aorta	Aorta
7	chr3:45934600-45946200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:45935400-45941200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:45935400-45945000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:45936000-45947600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:45936200-45939400	Enhancers	Hela-S3	cervix
12	chr3:45936400-45939200	Enhancers	HMEC	breast
13	chr3:45936600-45938600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr3:45936600-45940200	Genic enhancers	Thymus	Thymus
15	chr3:45936600-45945800	Weak transcription	Primary B cells from cord blood	blood
16	chr3:45936600-45950200	Genic enhancers	Fetal Thymus	thymus
17	chr3:45936800-45939600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:45936800-45941000	Weak transcription	Primary T cells from cord blood	blood
19	chr3:45936800-45946200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:45937400-45939200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:45937600-45938200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
22	chr3:45937600-45938600	Enhancers	Small Intestine	intestine
23	chr3:45937600-45939000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:45937600-45939000	Enhancers	Fetal Lung	lung
25	chr3:45937600-45939200	Enhancers	Placenta	Placenta
26	chr3:45937800-45938200	Enhancers	Duodenum Mucosa	Duodenum
27	chr3:45937800-45938600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr3:45937800-45938600	Enhancers	NHEK	skin
29	chr3:45937800-45938800	Enhancers	NH-A	brain
30	chr3:45937800-45939000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:45937800-45939200	Enhancers	Fetal Stomach	stomach
32	chr3:45937800-45939400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:45937800-45939400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr3:45937800-45939400	Enhancers	Esophagus	oesophagus
35	chr3:45938000-45938800	Enhancers	HSMM	muscle
36	chr3:45938000-45939000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:45938000-45939000	Enhancers	Muscle Satellite Cultured Cells	--
38	chr3:45938000-45939000	Enhancers	NHLF	lung

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