Variant report

Variant	rs17499691
Chromosome Location	chr15:50428741-50428742
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50428036..50430534-chr15:50437642..50439457,2	MCF-7	breast:
2	chr15:50420970..50423759-chr15:50428011..50430538,2	MCF-7	breast:
3	chr15:50418543..50420300-chr15:50426585..50429061,2	MCF-7	breast:
4	chr15:50168979..50170922-chr15:50428589..50430451,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10519261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124609	1.00[ASN][1000 genomes]
rs11630182	1.00[ASN][1000 genomes]
rs11632154	1.00[ASN][1000 genomes]
rs11636227	1.00[ASN][1000 genomes]
rs11637894	1.00[ASN][1000 genomes]
rs12898586	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906611	1.00[ASN][1000 genomes]
rs12906623	0.89[AFR][1000 genomes]
rs12907171	1.00[ASN][1000 genomes]
rs12907571	1.00[ASN][1000 genomes]
rs12910217	0.81[GIH][hapmap]
rs12912492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912519	0.89[AFR][1000 genomes]
rs12916163	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648347	1.00[ASN][1000 genomes]
rs17415291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415452	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415911	1.00[ASN][1000 genomes]
rs17499601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17499837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414023	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28419389	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28626417	1.00[ASN][1000 genomes]
rs28689603	1.00[ASN][1000 genomes]
rs28726225	1.00[ASN][1000 genomes]
rs28883893	1.00[ASN][1000 genomes]
rs34398655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34958490	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35036853	0.89[EUR][1000 genomes]
rs35607381	1.00[ASN][1000 genomes]
rs35616430	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35796860	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020328	1.00[ASN][1000 genomes]
rs62023188	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62023189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493403	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71469679	1.00[ASN][1000 genomes]
rs71469681	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163792	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166848	0.81[GIH][hapmap]
rs8034200	1.00[ASN][1000 genomes]
rs8036098	0.89[AFR][1000 genomes]
rs9707844	0.94[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920455	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv569395	chr15:50345393-50437494	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv904208	chr15:50428495-50457858	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17499691	SECISBP2L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50424200-50429000	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr15:50425200-50429000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:50425800-50428800	Enhancers	Hela-S3	cervix
4	chr15:50425800-50430800	Enhancers	NHDF-Ad	bronchial
5	chr15:50426000-50428800	Enhancers	Primary hematopoietic stem cells	blood
6	chr15:50426000-50429000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:50426000-50429400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr15:50426000-50430600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:50426000-50430800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:50426400-50430400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:50426400-50430400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr15:50426400-50430600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:50426400-50430600	Enhancers	NHLF	lung
14	chr15:50426400-50430800	Enhancers	Osteobl	bone
15	chr15:50426600-50429000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:50426800-50429000	Enhancers	Stomach Smooth Muscle	stomach
17	chr15:50427000-50428800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:50427200-50429800	Weak transcription	HUVEC	blood vessel
19	chr15:50427600-50429200	Enhancers	Fetal Stomach	stomach
20	chr15:50427600-50429400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:50427800-50429400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:50427800-50429800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:50427800-50429800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:50427800-50429800	Weak transcription	HSMM	muscle
25	chr15:50427800-50429800	Weak transcription	NH-A	brain
26	chr15:50427800-50436400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:50428000-50429000	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr15:50428000-50429200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:50428000-50429200	Weak transcription	HMEC	breast
30	chr15:50428000-50429200	Weak transcription	K562	blood
31	chr15:50428000-50429200	Weak transcription	NHEK	skin
32	chr15:50428200-50428800	Enhancers	A549	lung
33	chr15:50428400-50428800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:50428400-50429400	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:50428400-50430400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:50428600-50428800	Enhancers	Rectal Smooth Muscle	rectum
37	chr15:50428600-50429600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:50428600-50429800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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