Variant report

Variant	rs664608
Chromosome Location	chr13:53453283-53453284
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12100313	0.96[ASN][1000 genomes]
rs1274580	0.94[ASN][1000 genomes]
rs1274581	0.95[ASN][1000 genomes]
rs1274582	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1323117	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1323118	0.86[ASN][1000 genomes]
rs1359046	0.85[EUR][1000 genomes]
rs1885848	0.96[ASN][1000 genomes]
rs1923853	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2764035	0.95[ASN][1000 genomes]
rs2897999	0.96[ASN][1000 genomes]
rs471680	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886022	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs489654	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs496890	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508523	0.94[ASN][1000 genomes]
rs525135	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs537874	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs540528	0.94[ASN][1000 genomes]
rs572545	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs582583	0.90[EUR][1000 genomes]
rs604105	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs615225	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs629671	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs636937	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs646902	0.93[ASN][1000 genomes]
rs648146	0.93[ASN][1000 genomes]
rs648232	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs649523	0.94[ASN][1000 genomes]
rs6561691	0.83[ASN][1000 genomes]
rs676284	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs912091	0.80[ASN][1000 genomes]
rs9316593	0.88[ASN][1000 genomes]
rs9316594	0.83[ASN][1000 genomes]
rs9527030	0.86[ASN][1000 genomes]
rs9536315	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9591474	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9596705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9596709	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9596710	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9788390	0.96[ASN][1000 genomes]
rs9788403	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv455889	chr13:53419139-53466127	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	nsv561661	chr13:53419139-53466127	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs664608	EBPL	cis	parietal	SCAN
rs664608	LOC220429	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53448800-53455200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:53449800-53455000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:53450000-53454600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:53451400-53455600	Weak transcription	Pancreas	Pancrea
5	chr13:53452800-53453600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
6	chr13:53452800-53455600	Enhancers	Fetal Stomach	stomach
7	chr13:53453000-53453400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
8	chr13:53453000-53454200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
9	chr13:53453000-53454200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
10	chr13:53453000-53454600	Enhancers	Brain Germinal Matrix	brain
11	chr13:53453200-53455000	Weak transcription	Fetal Muscle Leg	muscle
12	chr13:53453200-53466600	Weak transcription	Fetal Brain Female	brain

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