Variant report

Variant	rs9316593
Chromosome Location	chr13:53468335-53468336
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	chr13:53461940..53463906-chr13:53466644..53468336,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12100313	0.84[ASN][1000 genomes]
rs1274580	0.82[ASN][1000 genomes]
rs1274581	0.83[ASN][1000 genomes]
rs1274582	0.84[ASN][1000 genomes]
rs1323117	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1885848	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2764035	0.83[ASN][1000 genomes]
rs2897999	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs471680	0.83[ASN][1000 genomes]
rs4886022	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886033	0.82[ASN][1000 genomes]
rs489654	0.83[ASN][1000 genomes]
rs496890	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs508523	0.82[ASN][1000 genomes]
rs525135	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs537874	0.84[ASN][1000 genomes]
rs540528	0.82[ASN][1000 genomes]
rs572545	0.80[ASN][1000 genomes]
rs604105	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs615225	0.83[ASN][1000 genomes]
rs629671	0.83[ASN][1000 genomes]
rs636937	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs646902	0.81[ASN][1000 genomes]
rs648146	0.81[ASN][1000 genomes]
rs648232	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs649523	0.82[ASN][1000 genomes]
rs6561691	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs664608	0.88[ASN][1000 genomes]
rs676284	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs912091	0.92[ASN][1000 genomes]
rs9316594	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9527030	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9536315	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596705	0.84[ASN][1000 genomes]
rs9596709	0.97[ASN][1000 genomes]
rs9596710	0.97[ASN][1000 genomes]
rs9788390	0.84[ASN][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	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv900090	chr13:53429453-53495715	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9316593	C20orf72	trans	cerebellum	SCAN
rs9316593	OLFM4	cis	cerebellum	SCAN
rs9316593	CAB39L	cis	parietal	SCAN
rs9316593	DLEU1	cis	cerebellum	SCAN
rs9316593	RB1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53461600-53471200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:53463000-53471200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:53466000-53468400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:53466400-53471000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr13:53466800-53471000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr13:53466800-53471200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr13:53466800-53472400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:53467000-53469600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:53467000-53471000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr13:53467200-53471000	Weak transcription	Fetal Brain Female	brain
11	chr13:53467400-53469800	Weak transcription	Fetal Stomach	stomach
12	chr13:53467400-53471000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr13:53468000-53469000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:53468000-53469200	Enhancers	Fetal Brain Male	brain
15	chr13:53468200-53470200	Weak transcription	Fetal Muscle Leg	muscle

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