Variant report

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:114026056..114028346-chr2:114029301..114030897,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSD4-1	chr2:114023053-114034158	ENSG00000189223.9

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1021409	0.88[ASN][1000 genomes]
rs11123176	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11123177	0.82[AMR][1000 genomes]
rs11123179	0.82[AMR][1000 genomes]
rs11685107	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11685421	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11691437	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471722	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12475140	0.81[AMR][1000 genomes]
rs12476056	0.80[AMR][1000 genomes]
rs12478795	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12999288	0.88[ASN][1000 genomes]
rs13015130	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1900216	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002510	0.81[AMR][1000 genomes]
rs35006857	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4848321	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877202	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895416	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895417	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935365	0.84[AMR][1000 genomes];1.00[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	nsv508162	chr2:113983043-114099966	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv535895	chr2:114015492-114037018	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv874901	chr2:114022569-114079565	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv998204	chr2:114023917-114075446	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12476331	AC016683.6	cis	Whole Blood	GTEx
rs12476331	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs12476331	PAX8	cis	lung	GTEx
rs12476331	AC016683.6	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:114010200-114030400	Weak transcription	GM12878-XiMat	blood
2	chr2:114023200-114039800	Weak transcription	Gastric	stomach
3	chr2:114024000-114030000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:114026600-114033400	Weak transcription	Lung	lung
5	chr2:114026600-114034400	Weak transcription	Pancreas	Pancrea
6	chr2:114029000-114030200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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