Variant report

Variant	rs12640049
Chromosome Location	chr4:110320011-110320012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110052875..110055808-chr4:110318973..110320982,2	K562	blood:

Extended variants
information (count: 145 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10000545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10002595	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10005355	0.86[ASN][1000 genomes]
rs10016533	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10028250	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10155127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10516558	0.93[CEU][hapmap];0.92[GIH][hapmap];0.86[ASN][1000 genomes]
rs11098033	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11098035	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11929713	0.83[CEU][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11930655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11933172	0.81[CHD][hapmap]
rs11933971	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11934486	1.00[ASN][1000 genomes]
rs11935440	0.96[ASN][1000 genomes]
rs11935629	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs11938593	0.96[ASN][1000 genomes]
rs11941344	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11942140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11942291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11942858	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11942928	0.96[ASN][1000 genomes]
rs11943384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11943430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11944375	0.96[ASN][1000 genomes]
rs11944427	0.96[ASN][1000 genomes]
rs11944659	1.00[ASN][1000 genomes]
rs12639832	1.00[ASN][1000 genomes]
rs12640161	0.92[ASN][1000 genomes]
rs12642304	0.86[ASN][1000 genomes]
rs12643055	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12643844	0.86[ASN][1000 genomes]
rs12644055	0.82[CHB][hapmap];0.96[ASN][1000 genomes]
rs12647695	0.96[ASN][1000 genomes]
rs12648138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12648965	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12650654	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12650873	0.96[ASN][1000 genomes]
rs13103034	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13110999	0.86[CEU][hapmap]
rs13113384	0.84[AMR][1000 genomes]
rs13119700	0.84[AMR][1000 genomes]
rs13122093	0.86[CEU][hapmap]
rs13123618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13125368	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13128124	0.86[ASN][1000 genomes]
rs13128221	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs13128445	0.85[MEX][hapmap]
rs13134239	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13138833	0.87[AMR][1000 genomes]
rs13140373	0.86[CEU][hapmap]
rs13141701	0.86[ASN][1000 genomes]
rs13142698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13143825	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13145066	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1509314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1509315	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17040410	0.96[ASN][1000 genomes]
rs17040436	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17040439	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17040461	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17040488	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17040510	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs17585970	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs17619262	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2346014	0.87[AMR][1000 genomes]
rs28521972	0.83[ASN][1000 genomes]
rs28585579	0.82[AMR][1000 genomes]
rs28628718	0.84[AMR][1000 genomes]
rs28681408	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34153531	0.86[ASN][1000 genomes]
rs34224638	0.86[ASN][1000 genomes]
rs34274964	0.86[ASN][1000 genomes]
rs34441811	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34482781	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34505473	0.82[EUR][1000 genomes]
rs34836476	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35110951	0.86[ASN][1000 genomes]
rs35359830	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35473144	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35594044	0.86[ASN][1000 genomes]
rs35762958	0.86[ASN][1000 genomes]
rs35791246	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35940980	0.86[ASN][1000 genomes]
rs36009064	0.82[ASN][1000 genomes]
rs36115572	0.86[ASN][1000 genomes]
rs3775962	0.86[ASN][1000 genomes]
rs60957336	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61004219	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61242473	0.84[ASN][1000 genomes]
rs61439452	0.94[ASN][1000 genomes]
rs61553525	0.96[ASN][1000 genomes]
rs6533426	0.87[AMR][1000 genomes]
rs6533428	0.94[ASN][1000 genomes]
rs6533429	0.96[ASN][1000 genomes]
rs6533434	1.00[MEX][hapmap]
rs66642182	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66667140	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67473696	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs68041341	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6812469	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6815455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6817954	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6818911	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs6823032	0.86[ASN][1000 genomes]
rs6825928	0.88[MEX][hapmap]
rs6827006	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6833753	0.84[ASN][1000 genomes]
rs6835683	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6837199	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6841133	0.84[AMR][1000 genomes]
rs6841198	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6841222	0.84[AMR][1000 genomes]
rs6845371	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6848452	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6851517	0.96[ASN][1000 genomes]
rs6852037	0.86[ASN][1000 genomes]
rs6856291	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6856446	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71603033	0.87[EUR][1000 genomes]
rs72896619	0.92[ASN][1000 genomes]
rs72896622	0.92[ASN][1000 genomes]
rs72896625	0.92[ASN][1000 genomes]
rs72896629	0.92[ASN][1000 genomes]
rs72896632	0.84[ASN][1000 genomes]
rs73838809	0.86[ASN][1000 genomes]
rs7436583	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7436745	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7440371	0.96[ASN][1000 genomes]
rs7440570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7675602	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7679836	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7680296	0.83[EUR][1000 genomes]
rs7687245	1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs876464	0.87[AMR][1000 genomes]
rs9985632	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9985964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9993228	0.87[AMR][1000 genomes]
rs9994676	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9994985	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9996432	0.87[AMR][1000 genomes]
rs9999570	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];0.86[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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv1799708	chr4:110309234-110333106	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12640049	SEC24B	cis	multi-tissue	Pritchard

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110311200-110327800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:110311600-110331400	Weak transcription	HSMMtube	muscle
3	chr4:110317200-110321800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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