Variant report

Variant	rs900054
Chromosome Location	chr15:40546291-40546292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40529010..40532751-chr15:40545483..40549200,3	MCF-7	breast:
2	chr15:40546251..40550526-chr15:40556944..40560237,5	K562	blood:

Variant related genes	Relation type
ENSG00000137843	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1048163	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048164	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11634057	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634409	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636147	1.00[JPT][hapmap]
rs11638662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638733	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12050520	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17733008	1.00[JPT][hapmap]
rs2018127	1.00[JPT][hapmap]
rs2289327	1.00[JPT][hapmap]
rs55799438	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55863440	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55974545	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731469	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72731470	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040419	1.00[JPT][hapmap]

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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs900054	RPAP1	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40545200-40547600	Strong transcription	HMEC	breast
2	chr15:40545800-40546400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr15:40545800-40546600	Enhancers	Esophagus	oesophagus
4	chr15:40545800-40546600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
5	chr15:40545800-40549600	Strong transcription	NHEK	skin
6	chr15:40546000-40546400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:40546000-40546400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
8	chr15:40546000-40546600	Bivalent Enhancer	Fetal Intestine Large	intestine
9	chr15:40546000-40547400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:40546000-40547800	Enhancers	Pancreas	Pancrea
11	chr15:40546000-40548000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:40546000-40549200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:40546000-40550600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:40546000-40558400	Weak transcription	Brain Anterior Caudate	brain
15	chr15:40546000-40558600	Weak transcription	Brain Angular Gyrus	brain
16	chr15:40546000-40571800	Weak transcription	Right Ventricle	heart
17	chr15:40546200-40546400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr15:40546200-40546400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:40546200-40546400	Enhancers	Colonic Mucosa	Colon
20	chr15:40546200-40546400	Bivalent/Poised TSS	Fetal Brain Male	brain
21	chr15:40546200-40546800	Bivalent Enhancer	Fetal Intestine Small	intestine
22	chr15:40546200-40547000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:40546200-40547800	Weak transcription	Gastric	stomach
24	chr15:40546200-40548400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:40546200-40549800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:40546200-40551600	Enhancers	Placenta	Placenta
27	chr15:40546200-40552600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr15:40546200-40568200	Weak transcription	Duodenum Mucosa	Duodenum

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