Variant report

Variant	rs248678
Chromosome Location	chr5:60337858-60337859
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	chr5:60308495..60310817-chr5:60337811..60340272,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10471503	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10939874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs11951504	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11951606	0.91[CEU][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12696976	0.92[ASN][1000 genomes]
rs13189346	0.88[ASN][1000 genomes]
rs13357828	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs158563	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158565	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158566	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158567	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158568	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158569	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158925	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158926	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs158928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1609041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162229	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs162231	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162232	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162233	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162235	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162236	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162237	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs162239	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162240	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162250	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs167912	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs170658	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs182351	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867597	0.88[ASN][1000 genomes]
rs2306350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2306351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs248679	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248680	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2619891	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2619892	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs290504	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs290505	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs290508	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2909851	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928243	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2928246	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2950232	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295556	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295557	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs295565	0.91[EUR][1000 genomes]
rs295567	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs329614	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs329615	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs329618	0.89[EUR][1000 genomes]
rs329619	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329620	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329627	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34425764	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34595	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34598	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs34599	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34640	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34641	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35319315	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35383830	0.81[EUR][1000 genomes]
rs3797562	0.89[ASN][1000 genomes]
rs4647078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4647108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4647135	0.89[ASN][1000 genomes]
rs4647168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4700398	0.86[ASN][1000 genomes]
rs4700401	0.88[ASN][1000 genomes]
rs6449506	0.84[ASN][1000 genomes]
rs6449507	0.89[ASN][1000 genomes]
rs6449508	0.89[ASN][1000 genomes]
rs6449509	1.00[CEU][hapmap]
rs6449510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6871236	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7445953	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7700975	0.89[ASN][1000 genomes]
rs7714071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7717909	0.88[ASN][1000 genomes]
rs7731760	0.88[ASN][1000 genomes]
rs9291704	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv881717	chr5:60141245-60372582	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869065	chr5:60180775-60428760	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv881721	chr5:60232646-60344399	Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv598313	chr5:60247815-60374912	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv881722	chr5:60266875-60384171	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1019307	chr5:60295350-60409077	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs248678	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60323000-60347000	Weak transcription	Primary B cells from cord blood	blood
2	chr5:60324600-60354000	Weak transcription	Primary T cells from cord blood	blood
3	chr5:60326000-60400800	Weak transcription	Left Ventricle	heart
4	chr5:60326200-60339400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:60335600-60343800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr5:60336000-60339400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:60337400-60339200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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