Variant report

Variant	rs248680
Chromosome Location	chr5:60361654-60361655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10471503	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11951504	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11951606	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12696976	0.82[ASN][1000 genomes]
rs13357828	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs158563	0.88[ASN][1000 genomes]
rs158565	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs158566	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs158567	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs158568	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs158569	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs158916	0.88[ASN][1000 genomes]
rs158920	0.88[ASN][1000 genomes]
rs158925	0.88[ASN][1000 genomes]
rs158926	0.88[ASN][1000 genomes]
rs158928	0.82[ASN][1000 genomes]
rs1609041	0.88[ASN][1000 genomes]
rs162229	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162231	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162232	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162233	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162235	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162236	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs162237	0.86[ASN][1000 genomes]
rs162239	0.88[ASN][1000 genomes]
rs162240	0.88[ASN][1000 genomes]
rs162250	0.88[ASN][1000 genomes]
rs167912	0.88[ASN][1000 genomes]
rs170658	0.83[ASN][1000 genomes]
rs182351	0.88[ASN][1000 genomes]
rs248678	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248679	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2619891	0.88[ASN][1000 genomes]
rs2619892	0.88[ASN][1000 genomes]
rs290504	0.88[ASN][1000 genomes]
rs290505	0.88[ASN][1000 genomes]
rs290508	0.81[ASN][1000 genomes]
rs2909851	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2928243	0.88[ASN][1000 genomes]
rs2928246	0.88[ASN][1000 genomes]
rs2950232	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs295556	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs295557	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs295565	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs295567	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs329614	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs329615	0.82[ASN][1000 genomes]
rs329619	0.88[ASN][1000 genomes]
rs329620	0.88[ASN][1000 genomes]
rs329627	0.88[ASN][1000 genomes]
rs34425764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34595	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34598	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34640	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34641	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35319315	0.82[ASN][1000 genomes]
rs4647078	0.82[ASN][1000 genomes]
rs6871236	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9291704	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	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
7	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
8	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
rs248680	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60326000-60400800	Weak transcription	Left Ventricle	heart
2	chr5:60347200-60379200	Weak transcription	Ovary	ovary
3	chr5:60349400-60370800	Weak transcription	HSMM	muscle
4	chr5:60350400-60362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:60350400-60371400	Weak transcription	NHDF-Ad	bronchial
6	chr5:60350600-60378600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:60350800-60396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:60357800-60369000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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