Variant report

Variant	rs1650779
Chromosome Location	chr5:68453465-68453466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:68453342-68453468	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68452033..68456569-chr5:68461553..68463610,4	K562	blood:
2	chr5:68452099..68454629-chr5:68466441..68468788,2	K562	blood:
3	chr5:68450558..68453533-chr5:68461225..68464745,3	K562	blood:

Variant related genes	Relation type
ENSG00000220986	TF binding region
ENSG00000134057	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs100192	0.81[ASN][1000 genomes]
rs10940209	0.87[ASN][1000 genomes]
rs10940210	0.86[ASN][1000 genomes]
rs11748974	0.83[ASN][1000 genomes]
rs13175606	0.94[ASN][1000 genomes]
rs151589	0.94[ASN][1000 genomes]
rs163442	0.81[ASN][1000 genomes]
rs163443	0.81[ASN][1000 genomes]
rs163444	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs164386	0.81[ASN][1000 genomes]
rs164388	0.81[ASN][1000 genomes]
rs164390	0.81[ASN][1000 genomes]
rs164715	0.94[ASN][1000 genomes]
rs1683831	0.85[ASN][1000 genomes]
rs171212	0.87[ASN][1000 genomes]
rs184747	0.94[ASN][1000 genomes]
rs2130757	0.87[ASN][1000 genomes]
rs2171148	0.87[ASN][1000 genomes]
rs2172056	0.87[ASN][1000 genomes]
rs2291519	0.87[ASN][1000 genomes]
rs2291520	0.87[ASN][1000 genomes]
rs2450230	0.90[ASN][1000 genomes]
rs2450246	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28506805	0.85[ASN][1000 genomes]
rs28602964	0.85[ASN][1000 genomes]
rs2930945	0.91[ASN][1000 genomes]
rs2930949	0.87[ASN][1000 genomes]
rs2930951	0.87[ASN][1000 genomes]
rs2932767	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2932772	0.92[ASN][1000 genomes]
rs2932773	0.92[ASN][1000 genomes]
rs2932775	0.92[ASN][1000 genomes]
rs2932776	0.92[ASN][1000 genomes]
rs2932782	0.87[ASN][1000 genomes]
rs2972361	0.87[ASN][1000 genomes]
rs2972366	0.87[ASN][1000 genomes]
rs2972381	0.87[ASN][1000 genomes]
rs2972386	0.87[ASN][1000 genomes]
rs2972387	0.87[ASN][1000 genomes]
rs2972388	0.87[ASN][1000 genomes]
rs350099	0.81[ASN][1000 genomes]
rs350107	0.94[ASN][1000 genomes]
rs350109	0.93[ASN][1000 genomes]
rs350115	0.94[ASN][1000 genomes]
rs350116	0.87[ASN][1000 genomes]
rs350120	0.81[ASN][1000 genomes]
rs350122	0.87[ASN][1000 genomes]
rs350123	0.92[ASN][1000 genomes]
rs351424	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs352626	0.81[ASN][1000 genomes]
rs353656	0.92[ASN][1000 genomes]
rs375285	0.81[ASN][1000 genomes]
rs376768	0.81[ASN][1000 genomes]
rs379106	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs379434	0.81[ASN][1000 genomes]
rs386640	0.94[ASN][1000 genomes]
rs389686	0.85[ASN][1000 genomes]
rs389938	0.81[ASN][1000 genomes]
rs3934528	0.86[ASN][1000 genomes]
rs395122	0.81[ASN][1000 genomes]
rs4077460	0.86[ASN][1000 genomes]
rs419902	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4266362	0.85[ASN][1000 genomes]
rs4362903	0.86[ASN][1000 genomes]
rs437665	0.85[ASN][1000 genomes]
rs4421064	0.86[ASN][1000 genomes]
rs444305	0.82[ASN][1000 genomes]
rs4541612	0.84[ASN][1000 genomes]
rs4629549	0.86[ASN][1000 genomes]
rs476125	0.85[ASN][1000 genomes]
rs488498	0.86[ASN][1000 genomes]
rs603029	0.85[ASN][1000 genomes]
rs62373164	0.86[ASN][1000 genomes]
rs648489	0.81[ASN][1000 genomes]
rs651076	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs676879	0.88[ASN][1000 genomes]
rs6866993	0.86[ASN][1000 genomes]
rs6876783	0.86[ASN][1000 genomes]
rs693725	0.94[ASN][1000 genomes]
rs7719040	0.81[ASN][1000 genomes]
rs7733556	0.86[ASN][1000 genomes]
rs875459	0.81[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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv527990	chr5:68448694-68455166	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1650779	CCDC125	cis	Esophagus Mucosa	GTEx
rs1650779	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs1650779	CCDC125	cis	lung	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68443600-68462000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:68452800-68453800	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links