Variant report

Variant	rs460470
Chromosome Location	chr20:52681167-52681168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:52212827..52216446-chr20:52677595..52681391,3	MCF-7	breast:
2	chr20:52261605..52264321-chr20:52679495..52681960,2	MCF-7	breast:
3	chr20:46413659..46415494-chr20:52680026..52681756,2	MCF-7	breast:
4	chr17:56707565..56710367-chr20:52679434..52682124,8	MCF-7	breast:
5	chr20:46412316..46414537-chr20:52680963..52682540,2	MCF-7	breast:
6	chr17:57920042..57923174-chr20:52680014..52682936,4	MCF-7	breast:
7	chr20:52553947..52555886-chr20:52679638..52682394,3	MCF-7	breast:
8	chr20:52193423..52196094-chr20:52680219..52682403,2	MCF-7	breast:
9	chr17:56736755..56739038-chr20:52679388..52681171,2	MCF-7	breast:
10	chr20:52679591..52682376-chr20:52684226..52686968,2	K562	blood:
11	chr17:56735435..56738179-chr20:52680287..52682149,2	MCF-7	breast:
12	chr20:52679231..52682277-chr20:52687139..52688972,3	K562	blood:
13	chr17:59476912..59478517-chr20:52679687..52681644,2	MCF-7	breast:
14	chr20:52535496..52537138-chr20:52680677..52682336,2	MCF-7	breast:
15	chr17:59713148..59713900-chr20:52680664..52681503,2	MCF-7	breast:
16	chr17:56707956..56710519-chr20:52679502..52682472,2	MCF-7	breast:
17	chr20:52572107..52575056-chr20:52680520..52683373,2	MCF-7	breast:
18	chr20:52680642..52682938-chr20:55848441..55851071,2	MCF-7	breast:
19	chr20:52556569..52566193-chr20:52677353..52682397,12	MCF-7	breast:
20	chr20:52681034..52683636-chr20:53260094..53262163,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236352	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000196562	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000265595	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs103926	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1531486	0.82[YRI][hapmap]
rs1537439	0.83[YRI][hapmap]
rs290391	0.83[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs290392	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs290393	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs290430	0.99[ASN][1000 genomes]
rs290431	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs290432	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs290436	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs290441	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs290444	0.93[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs290445	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs290446	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs290448	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs290449	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3787547	0.80[YRI][hapmap]
rs3787550	0.82[YRI][hapmap]
rs394732	0.80[YRI][hapmap]
rs458674	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459376	0.83[YRI][hapmap]
rs460317	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460536	0.83[YRI][hapmap]
rs462041	0.83[YRI][hapmap]
rs462083	0.93[YRI][hapmap]
rs462174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462703	0.80[YRI][hapmap]
rs463420	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs463722	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs465096	0.83[YRI][hapmap]
rs467267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467321	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756021	0.87[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[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	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
3	esv2756743	chr20:52679137-52685208	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region miRNA	20 gene(s)	inside rSNPs	diseases
4	esv2758801	chr20:52679137-52685208	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs460470	BCAS1	Cis_1M	lymphoblastoid	RTeQTL
rs460470	BCAS1	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr20:52669400-52681800	Weak transcription	Gastric	stomach
3	chr20:52674400-52681200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:52674400-52682000	Weak transcription	Colonic Mucosa	Colon
5	chr20:52675000-52683000	Weak transcription	HepG2	liver
6	chr20:52678200-52683800	Weak transcription	HMEC	breast
7	chr20:52678200-52684400	Weak transcription	Fetal Stomach	stomach
8	chr20:52678400-52683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:52679200-52681600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr20:52679400-52683000	Weak transcription	HSMM	muscle
11	chr20:52679400-52683000	Weak transcription	NH-A	brain
12	chr20:52679600-52681400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr20:52679600-52682200	Enhancers	Primary B cells from peripheral blood	blood
14	chr20:52679600-52682200	Enhancers	Primary hematopoietic stem cells	blood
15	chr20:52679600-52682400	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr20:52679600-52682600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr20:52679800-52681400	Weak transcription	K562	blood
18	chr20:52679800-52682200	Weak transcription	Fetal Heart	heart
19	chr20:52679800-52683000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr20:52679800-52683000	Weak transcription	HSMMtube	muscle
21	chr20:52680000-52681400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr20:52680000-52682000	Weak transcription	Fetal Intestine Small	intestine
23	chr20:52680000-52683000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr20:52680200-52681600	Flanking Active TSS	GM12878-XiMat	blood
25	chr20:52680400-52684400	Enhancers	A549	lung
26	chr20:52680600-52681200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr20:52680800-52681200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr20:52680800-52681200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr20:52680800-52681400	Enhancers	iPS-20b Cell Line	embryonic stem cell
30	chr20:52680800-52682400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr20:52681000-52681200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr20:52681000-52681200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr20:52681000-52681600	Genic enhancers	Stomach Mucosa	stomach
34	chr20:52681000-52682200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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