Variant report

Variant	rs6059724
Chromosome Location	chr20:29833609-29833610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1080568	0.92[ASN][1000 genomes]
rs13045866	0.94[ASN][1000 genomes]
rs1474945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1884743	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1980582	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2076373	0.85[CHB][hapmap]
rs2076374	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs2076375	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2143191	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap]
rs2180566	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap]
rs2206381	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap]
rs2206382	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs2206383	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2223527	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2281554	0.83[CHB][hapmap]
rs2295500	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap]
rs2295501	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2376538	0.97[ASN][1000 genomes]
rs2376858	0.83[CHB][hapmap]
rs35293804	0.97[ASN][1000 genomes]
rs4243975	0.96[ASN][1000 genomes]
rs4300919	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap]
rs4333000	0.96[ASN][1000 genomes]
rs4525766	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4911191	0.95[ASN][1000 genomes]
rs4911211	0.92[ASN][1000 genomes]
rs4911274	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs4911306	0.84[CHB][hapmap]
rs4911329	0.85[CHB][hapmap];0.88[CHD][hapmap];0.80[JPT][hapmap]
rs4911432	0.96[ASN][1000 genomes]
rs4911529	0.94[ASN][1000 genomes]
rs4911530	0.95[ASN][1000 genomes]
rs4911531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4911555	0.90[ASN][1000 genomes]
rs4911557	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs5001275	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap]
rs6057649	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap]
rs6057678	0.81[AMR][1000 genomes]
rs6057860	0.97[ASN][1000 genomes]
rs6057963	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6058066	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6058399	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6058531	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6058905	0.91[AMR][1000 genomes]
rs6058918	0.83[JPT][hapmap]
rs6059128	0.83[CHB][hapmap]
rs6059238	0.97[ASN][1000 genomes]
rs6059332	0.80[ASN][1000 genomes]
rs6059335	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs6059667	0.93[AMR][1000 genomes]
rs6059891	0.89[AMR][1000 genomes]
rs6059955	0.96[ASN][1000 genomes]
rs6059977	0.97[ASN][1000 genomes]
rs6060006	0.99[ASN][1000 genomes]
rs6060100	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6061178	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap]
rs6061207	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6061213	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6087445	0.85[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap]
rs6087464	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs6087468	0.85[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs6087777	0.95[ASN][1000 genomes]
rs6087831	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6087852	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6087854	0.92[ASN][1000 genomes]
rs6087927	0.87[ASN][1000 genomes]
rs6088036	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs6088109	0.85[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs6088112	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs6088144	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs6088167	0.93[ASN][1000 genomes]
rs6088215	0.85[CHB][hapmap];0.90[CHD][hapmap];0.80[JPT][hapmap]
rs6088264	0.93[ASN][1000 genomes]
rs6088591	0.99[ASN][1000 genomes]
rs6088748	0.97[ASN][1000 genomes]
rs6089126	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6120006	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6120575	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6141536	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6141934	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs6142150	0.96[ASN][1000 genomes]
rs6142220	0.96[ASN][1000 genomes]
rs6142241	0.98[ASN][1000 genomes]
rs709045	0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap]
rs732861	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs734418	0.85[CHB][hapmap];0.93[CHD][hapmap]
rs760996	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs8183998	0.87[ASN][1000 genomes]
rs975075	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9798579	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3342568	chr20:29803909-29834289	ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
2	esv3362807	chr20:29803909-29834289	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
3	esv3392375	chr20:29803909-29834289	ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
4	esv3412704	chr20:29803909-29834289	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
5	esv3445374	chr20:29803909-29834289	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
6	esv3451819	chr20:29803909-29834389	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS	n/a	n/a	inside rSNPs	diseases
7	nsv964448	chr20:29803909-29857200	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv585887	chr20:29804208-29833609	ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
9	nsv585888	chr20:29804208-29844859	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
10	esv1800744	chr20:29804293-29860684	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1806005	chr20:29804293-29860684	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv1809844	chr20:29804293-29860684	Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv1821656	chr20:29804293-29860684	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv1829940	chr20:29804293-29860684	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv1836734	chr20:29804293-29860684	ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv1839077	chr20:29804293-29860684	ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	esv1850349	chr20:29804293-29860684	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv2485082	chr20:29806791-29833789	ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS	n/a	n/a	inside rSNPs	diseases
19	nsv869384	chr20:29833386-30605088	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	419 gene(s)	inside rSNPs	diseases
20	nsv833951	chr20:29833448-29878205	Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv458960	chr20:29833609-29912852	Active TSS ZNF genes & repeats Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv585909	chr20:29833609-29912852	Active TSS Weak transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv470546	chr20:29833609-30235302	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	385 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6059724	NECAB3	cis	parietal	SCAN
rs6059724	FRG1B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:29803800-29833800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr20:29833400-29835600	Weak transcription	Fetal Heart	heart
3	chr20:29833400-29839400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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