Variant report

Variant	rs11854975
Chromosome Location	chr15:75363876-75363877
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	chr15:75362436..75364878-chr15:75367523..75369824,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12101482	0.86[EUR][1000 genomes]
rs12148488	0.85[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12898551	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12899062	0.86[EUR][1000 genomes]
rs12900072	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12904227	0.86[EUR][1000 genomes]
rs1867148	0.86[EUR][1000 genomes]
rs1867149	0.86[EUR][1000 genomes]
rs2304902	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35078352	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35116156	0.82[ASN][1000 genomes]
rs3812945	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs4886417	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886648	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886655	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495144	0.86[EUR][1000 genomes]
rs6495150	0.85[EUR][1000 genomes]
rs6495151	0.85[EUR][1000 genomes]
rs67168917	0.85[EUR][1000 genomes]
rs7163362	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7163636	0.85[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs7167261	0.86[EUR][1000 genomes]
rs7181261	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8028129	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8039755	0.85[CEU][hapmap];0.86[EUR][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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11854975	SCAMP5	cis	Artery Tibial	GTEx
rs11854975	ULK3	cis	parietal	SCAN
rs11854975	THAP10	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75342600-75364800	Weak transcription	Primary T cells from cord blood	blood
2	chr15:75347000-75364000	Weak transcription	Brain Substantia Nigra	brain
3	chr15:75356800-75366600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr15:75357000-75365400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:75358400-75368600	Weak transcription	Aorta	Aorta
6	chr15:75359200-75366200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr15:75359600-75364400	Enhancers	GM12878-XiMat	blood
8	chr15:75360000-75370000	Weak transcription	Right Atrium	heart
9	chr15:75360600-75364800	Enhancers	Primary B cells from peripheral blood	blood
10	chr15:75360600-75366600	Enhancers	Primary B cells from cord blood	blood
11	chr15:75360800-75368200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:75361800-75365200	Weak transcription	Placenta	Placenta
13	chr15:75361800-75366800	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr15:75362400-75365200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr15:75362600-75364600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:75362800-75364200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:75363000-75368400	Weak transcription	HepG2	liver
18	chr15:75363200-75364200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:75363200-75365200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:75363600-75365600	Weak transcription	Fetal Thymus	thymus

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