Variant report

Variant	rs13147648
Chromosome Location	chr4:69901663-69901664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 146 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs10006595	0.93[EUR][1000 genomes]
rs10012215	0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10012240	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs10012607	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10019619	0.89[EUR][1000 genomes]
rs10021748	0.91[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10030220	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249520	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11725519	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501837	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509175	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12512098	0.88[EUR][1000 genomes]
rs12646327	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs12648808	0.89[ASN][1000 genomes]
rs12648830	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs13102620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13108709	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13116752	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127081	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13128177	0.84[EUR][1000 genomes]
rs13140844	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145165	0.89[EUR][1000 genomes]
rs13145304	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13147569	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1841055	0.89[EUR][1000 genomes]
rs1902923	0.84[EUR][1000 genomes]
rs1902929	0.81[CHB][hapmap]
rs2011000	0.81[EUR][1000 genomes]
rs2292524	0.92[ASN][1000 genomes]
rs2331627	0.89[EUR][1000 genomes]
rs28386872	0.93[EUR][1000 genomes]
rs28775401	0.94[ASN][1000 genomes]
rs28801471	0.95[ASN][1000 genomes]
rs3922514	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[ASN][1000 genomes]
rs4235106	0.90[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4235108	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4235111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235112	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4235113	0.92[ASN][1000 genomes]
rs4235114	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4299665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4299666	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4304032	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4305590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4312824	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351079	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4353969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365792	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377650	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4400060	0.90[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4400061	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4410590	0.89[ASN][1000 genomes]
rs4412058	0.89[ASN][1000 genomes]
rs4413468	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.96[ASN][1000 genomes]
rs4422474	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4440295	0.86[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4446390	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4481286	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4495114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4516791	0.89[ASN][1000 genomes]
rs4518318	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4583828	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4591680	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4600986	0.81[CHB][hapmap]
rs4607293	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4611997	0.88[ASN][1000 genomes]
rs4618380	0.87[ASN][1000 genomes]
rs4694159	0.88[ASN][1000 genomes]
rs4694160	0.89[ASN][1000 genomes]
rs4694490	0.88[EUR][1000 genomes]
rs4694491	0.89[EUR][1000 genomes]
rs4694551	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4694588	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4694597	0.89[ASN][1000 genomes]
rs4694599	0.89[ASN][1000 genomes]
rs4694602	0.89[ASN][1000 genomes]
rs4694604	0.89[ASN][1000 genomes]
rs4694605	0.89[ASN][1000 genomes]
rs4694607	0.89[ASN][1000 genomes]
rs4694610	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs4694611	0.89[ASN][1000 genomes]
rs4694612	0.86[ASN][1000 genomes]
rs55778959	0.81[ASN][1000 genomes]
rs56879009	0.89[ASN][1000 genomes]
rs57386454	0.97[ASN][1000 genomes]
rs58496756	0.86[ASN][1000 genomes]
rs60212682	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs60814050	0.94[ASN][1000 genomes]
rs61612343	0.89[ASN][1000 genomes]
rs6422321	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6422322	0.96[ASN][1000 genomes]
rs6600865	0.94[ASN][1000 genomes]
rs6600867	0.89[ASN][1000 genomes]
rs6820734	0.81[CHB][hapmap];0.93[CHD][hapmap]
rs6827511	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6828317	0.88[EUR][1000 genomes]
rs6831147	0.82[EUR][1000 genomes]
rs6837000	0.83[EUR][1000 genomes]
rs6839405	0.84[EUR][1000 genomes]
rs6843788	0.88[EUR][1000 genomes]
rs6850053	0.98[ASN][1000 genomes]
rs72851338	0.92[ASN][1000 genomes]
rs72851348	0.98[ASN][1000 genomes]
rs72852416	0.89[ASN][1000 genomes]
rs72852450	0.88[ASN][1000 genomes]
rs7434389	0.89[ASN][1000 genomes]
rs7435274	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7436912	0.89[ASN][1000 genomes]
rs7438033	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[ASN][1000 genomes]
rs7438808	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7439419	0.88[ASN][1000 genomes]
rs7441365	0.88[ASN][1000 genomes]
rs7441736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7442394	0.89[ASN][1000 genomes]
rs7442486	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs7654272	0.89[ASN][1000 genomes]
rs7657426	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7658748	0.89[ASN][1000 genomes]
rs7660019	0.83[ASN][1000 genomes]
rs7660021	0.82[ASN][1000 genomes]
rs7662632	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7666894	0.89[ASN][1000 genomes]
rs7673174	0.86[EUR][1000 genomes]
rs7674573	0.89[ASN][1000 genomes]
rs7674600	0.89[ASN][1000 genomes]
rs7677996	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7679418	0.89[ASN][1000 genomes]
rs7680156	0.89[ASN][1000 genomes]
rs7687336	0.89[ASN][1000 genomes]
rs7687692	0.83[ASN][1000 genomes]
rs7687725	0.89[ASN][1000 genomes]
rs7691258	0.86[EUR][1000 genomes]
rs7691445	0.86[EUR][1000 genomes]
rs7692377	0.89[ASN][1000 genomes]
rs7693166	0.88[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7698430	0.89[ASN][1000 genomes]
rs9715099	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999654	chr4:69661415-70132110	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	esv3420586	chr4:69680878-70322918	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv1067773	chr4:69718248-70715727	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	esv3468151	chr4:69718675-70322776	Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv3468153	chr4:69718675-70322776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv829962	chr4:69786869-69910283	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv594582	chr4:69827340-69988378	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv879379	chr4:69878929-69987249	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv964058	chr4:69900771-69904058	Enhancers Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13147648	Hs.479894	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:69900400-69901800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:69901600-69904600	Weak transcription	A549	lung

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