Variant report

Variant	rs226690
Chromosome Location	chr20:24777177-24777178
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	chr20:24630442..24631150-chr20:24777044..24777861,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11698988	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1883922	0.89[EUR][1000 genomes]
rs2244284	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2253628	0.83[EUR][1000 genomes]
rs226664	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs226667	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226668	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226669	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226670	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226671	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226672	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226674	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226675	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226676	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226677	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226678	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226679	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226687	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226688	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226697	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424646	0.88[EUR][1000 genomes]
rs2424649	0.89[EUR][1000 genomes]
rs2424650	0.88[EUR][1000 genomes]
rs2424661	0.83[EUR][1000 genomes]
rs2424662	0.90[EUR][1000 genomes]
rs2424663	0.83[EUR][1000 genomes]
rs2424664	0.83[EUR][1000 genomes]
rs2424665	0.83[EUR][1000 genomes]
rs2424666	0.83[EUR][1000 genomes]
rs2424667	0.83[EUR][1000 genomes]
rs2424668	0.83[EUR][1000 genomes]
rs2424669	0.90[EUR][1000 genomes]
rs2424670	0.81[EUR][1000 genomes]
rs2424671	0.82[EUR][1000 genomes]
rs2424672	0.83[EUR][1000 genomes]
rs2424673	0.82[EUR][1000 genomes]
rs2424674	0.89[EUR][1000 genomes]
rs2424675	0.82[EUR][1000 genomes]
rs2424678	0.90[EUR][1000 genomes]
rs2424689	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4813530	0.87[EUR][1000 genomes]
rs4813540	0.82[ASN][1000 genomes]
rs4815307	0.82[EUR][1000 genomes]
rs4815312	0.82[ASN][1000 genomes]
rs4815315	0.82[ASN][1000 genomes]
rs56103836	0.82[ASN][1000 genomes]
rs6036911	0.82[ASN][1000 genomes]
rs6049946	0.83[EUR][1000 genomes]
rs6049965	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6049976	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6049977	0.82[ASN][1000 genomes]
rs6049978	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6049983	0.82[ASN][1000 genomes]
rs6076275	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6076276	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6076277	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6083620	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6106942	0.90[EUR][1000 genomes]
rs6132765	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6138373	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73335420	0.82[ASN][1000 genomes]
rs73335440	0.82[ASN][1000 genomes]
rs73335460	0.82[ASN][1000 genomes]
rs743191	0.82[ASN][1000 genomes]
rs85804	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971957	0.88[EUR][1000 genomes]
rs974647	0.84[EUR][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	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1061412	chr20:24629468-24887869	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv544216	chr20:24629468-24887869	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1061281	chr20:24711635-24815107	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv544217	chr20:24711635-24815107	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv912825	chr20:24715544-24813345	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1061455	chr20:24733120-24861801	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv544218	chr20:24733120-24861801	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1059270	chr20:24741923-24787243	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs226690	GGTLC1	cis	parietal	SCAN
rs226690	C20orf3	cis	parietal	SCAN
rs226690	PPYR1	trans	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24774000-24783000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24775800-24777200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:24775800-24778000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr20:24776400-24777400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:24776400-24779000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr20:24776600-24779200	Weak transcription	HSMM	muscle
7	chr20:24776800-24779200	Weak transcription	HSMMtube	muscle
8	chr20:24777000-24777200	Enhancers	Spleen	Spleen
9	chr20:24777000-24778400	Enhancers	Fetal Kidney	kidney

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