Variant report

Variant	rs351424
Chromosome Location	chr5:68457386-68457387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68456891..68459039-chr5:68462526..68464339,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134057	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs100192	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10940209	0.89[ASN][1000 genomes]
rs10940210	0.87[ASN][1000 genomes]
rs11748974	0.85[ASN][1000 genomes]
rs13175606	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs151589	0.96[ASN][1000 genomes]
rs163442	0.81[ASN][1000 genomes]
rs163443	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs163444	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs164386	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs164388	0.81[ASN][1000 genomes]
rs164390	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs164715	0.96[ASN][1000 genomes]
rs1650779	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1683831	0.85[ASN][1000 genomes]
rs171212	0.88[ASN][1000 genomes]
rs184747	0.96[ASN][1000 genomes]
rs2130757	0.89[ASN][1000 genomes]
rs2171148	0.89[ASN][1000 genomes]
rs2172056	0.89[ASN][1000 genomes]
rs2291519	0.89[ASN][1000 genomes]
rs2291520	0.89[ASN][1000 genomes]
rs2450230	0.92[ASN][1000 genomes]
rs2450246	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28506805	0.85[ASN][1000 genomes]
rs28602964	0.87[ASN][1000 genomes]
rs2930945	0.92[ASN][1000 genomes]
rs2930949	0.89[ASN][1000 genomes]
rs2930951	0.89[ASN][1000 genomes]
rs2932767	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2932772	0.93[ASN][1000 genomes]
rs2932773	0.93[ASN][1000 genomes]
rs2932775	0.93[ASN][1000 genomes]
rs2932776	0.93[ASN][1000 genomes]
rs2932782	0.88[ASN][1000 genomes]
rs2972361	0.89[ASN][1000 genomes]
rs2972366	0.89[ASN][1000 genomes]
rs2972381	0.89[ASN][1000 genomes]
rs2972386	0.89[ASN][1000 genomes]
rs2972387	0.89[ASN][1000 genomes]
rs2972388	0.88[ASN][1000 genomes]
rs34935424	0.81[ASN][1000 genomes]
rs350099	0.81[ASN][1000 genomes]
rs350104	0.88[YRI][hapmap]
rs350107	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs350109	0.94[ASN][1000 genomes]
rs350115	0.96[ASN][1000 genomes]
rs350116	0.88[ASN][1000 genomes]
rs350120	0.81[ASN][1000 genomes]
rs350122	0.88[ASN][1000 genomes]
rs350123	0.93[ASN][1000 genomes]
rs352626	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs353656	0.94[ASN][1000 genomes]
rs375285	0.81[ASN][1000 genomes]
rs376768	0.81[ASN][1000 genomes]
rs379106	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379434	0.81[ASN][1000 genomes]
rs386640	0.96[ASN][1000 genomes]
rs389686	0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs389938	0.81[ASN][1000 genomes]
rs3934528	0.87[ASN][1000 genomes]
rs395122	0.81[ASN][1000 genomes]
rs4077460	0.87[ASN][1000 genomes]
rs419902	0.96[ASN][1000 genomes]
rs4266362	0.86[ASN][1000 genomes]
rs4362903	0.87[ASN][1000 genomes]
rs437665	0.95[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4421064	0.87[ASN][1000 genomes]
rs444305	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs4541612	0.85[ASN][1000 genomes]
rs4629549	0.88[ASN][1000 genomes]
rs476125	0.85[ASN][1000 genomes]
rs488498	0.87[ASN][1000 genomes]
rs4976189	0.80[ASN][1000 genomes]
rs603029	0.87[ASN][1000 genomes]
rs62373164	0.87[ASN][1000 genomes]
rs6450029	0.81[ASN][1000 genomes]
rs648489	0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs651076	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs676879	0.89[ASN][1000 genomes]
rs6866993	0.88[ASN][1000 genomes]
rs6873869	0.81[ASN][1000 genomes]
rs6876783	0.87[ASN][1000 genomes]
rs693725	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs7719040	0.81[ASN][1000 genomes]
rs7733556	0.88[ASN][1000 genomes]
rs875459	0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs351424	CCDC125	cis	Muscle Skeletal	GTEx
rs351424	GUSBP3	cis	Whole Blood	GTEx
rs351424	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs351424	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	chr5:68453800-68462000	Weak transcription	K562	blood

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