Variant report

Variant	rs6050122
Chromosome Location	chr20:24893947-24893948
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	chr20:24892772..24894924-chr20:24896880..24898878,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1029031	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1029033	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1113872	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11905160	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12151907	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12479636	1.00[ASN][1000 genomes]
rs1331285	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1331290	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1411892	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1411894	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1411895	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1831483	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1888655	0.83[EUR][1000 genomes]
rs2064404	1.00[CHB][hapmap]
rs28861375	0.87[AMR][1000 genomes]
rs28876699	0.82[AMR][1000 genomes]
rs4239751	1.00[CHB][hapmap]
rs4462847	1.00[ASN][1000 genomes]
rs4502500	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815358	1.00[CHB][hapmap]
rs4815359	1.00[CHB][hapmap]
rs55702326	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56106395	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56179484	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56183883	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036943	0.85[EUR][1000 genomes]
rs6036946	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6036951	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6036955	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6036967	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6036968	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6036970	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6036971	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6036972	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050007	0.82[EUR][1000 genomes]
rs6050051	0.83[EUR][1000 genomes]
rs6050058	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6050070	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6050073	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6050074	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6050114	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050115	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050116	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6050117	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6050119	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6050120	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6050121	1.00[ASN][1000 genomes]
rs6050124	1.00[ASN][1000 genomes]
rs6050125	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050127	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076290	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6076292	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6076299	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6083652	0.87[EUR][1000 genomes]
rs6083656	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6083658	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6083697	1.00[CHB][hapmap]
rs6083714	1.00[CHB][hapmap]
rs6106968	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6106969	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114915	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6114918	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6114921	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62215832	0.88[EUR][1000 genomes]
rs6515538	0.83[EUR][1000 genomes]
rs761368	1.00[CHB][hapmap]
rs765834	1.00[CHB][hapmap]
rs885402	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs914309	1.00[ASN][1000 genomes]
rs914310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914313	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914315	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944503	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961218	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv432115	chr20:24871385-24915839	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1058559	chr20:24880415-24923818	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1061536	chr20:24880777-24930642	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1060158	chr20:24887819-24918081	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1066090	chr20:24887819-24923818	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1065568	chr20:24887819-24925706	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv510783	chr20:24889192-24941933	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6050122	GGTLC1	cis	parietal	SCAN
rs6050122	C20orf3	cis	parietal	SCAN
rs6050122	C20orf191	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24891800-24896000	Weak transcription	Spleen	Spleen
2	chr20:24892600-24898600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr20:24893600-24894000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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