Variant report

Variant	rs2424557
Chromosome Location	chr20:23422159-23422160
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23415648..23417559-chr20:23421207..23423158,2	MCF-7	breast:
2	chr20:23422154..23423090-chr20:23586925..23587808,6	MCF-7	breast:
3	chr20:23329921..23332820-chr20:23421116..23423226,2	MCF-7	breast:
4	chr20:23421799..23423146-chr20:23586414..23588198,22	MCF-7	breast:
5	chr20:23422153..23424654-chr20:23586384..23588911,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132661	Chromatin interaction
ENSG00000173335	Chromatin interaction
ENSG00000234832	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1419005	0.87[CEU][hapmap];0.81[MEX][hapmap]
rs1419009	0.87[EUR][1000 genomes]
rs1419010	0.87[EUR][1000 genomes]
rs16985308	0.85[EUR][1000 genomes]
rs1936013	1.00[CEU][hapmap];0.82[MEX][hapmap];0.87[EUR][1000 genomes]
rs2004288	0.81[AMR][1000 genomes]
rs2051093	0.87[EUR][1000 genomes]
rs2144381	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2224074	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2236022	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2249943	0.87[EUR][1000 genomes]
rs2251145	0.87[EUR][1000 genomes]
rs2252824	1.00[CEU][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs2275787	0.84[EUR][1000 genomes]
rs2275788	0.84[EUR][1000 genomes]
rs2281429	1.00[CEU][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2424528	0.85[EUR][1000 genomes]
rs2424530	0.87[EUR][1000 genomes]
rs2424531	1.00[CEU][hapmap];0.82[MEX][hapmap];0.87[EUR][1000 genomes]
rs2424532	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2424534	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2424535	0.81[EUR][1000 genomes]
rs2424536	1.00[CEU][hapmap];0.82[MEX][hapmap];0.87[EUR][1000 genomes]
rs2424537	0.87[EUR][1000 genomes]
rs2424539	1.00[CEU][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2424540	0.84[EUR][1000 genomes]
rs2424541	0.86[EUR][1000 genomes]
rs2424544	0.87[EUR][1000 genomes]
rs2424545	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2424546	0.87[EUR][1000 genomes]
rs2424548	0.87[EUR][1000 genomes]
rs2424549	0.87[EUR][1000 genomes]
rs2424550	0.87[EUR][1000 genomes]
rs2424551	0.86[EUR][1000 genomes]
rs2424552	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2424554	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2424556	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3746734	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4813493	0.87[EUR][1000 genomes]
rs4813495	0.87[EUR][1000 genomes]
rs4815199	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4815203	0.87[EUR][1000 genomes]
rs6036387	0.81[LWK][hapmap]
rs6036393	0.82[LWK][hapmap]
rs6048748	0.86[LWK][hapmap]
rs6076057	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs6076059	0.87[CEU][hapmap];0.82[MEX][hapmap]
rs6076060	0.93[LWK][hapmap]
rs6076069	0.93[LWK][hapmap]
rs6076071	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6076073	0.87[EUR][1000 genomes]
rs6083082	0.86[LWK][hapmap]
rs6083084	0.87[CEU][hapmap]
rs6083085	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs6083087	0.84[EUR][1000 genomes]
rs6083088	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6083092	0.85[EUR][1000 genomes]
rs6083095	0.84[EUR][1000 genomes]
rs6083099	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6083100	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6083104	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6083110	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6083111	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6083119	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6114085	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132604	0.85[EUR][1000 genomes]
rs6132607	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6132612	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6137905	0.84[EUR][1000 genomes]
rs6137908	1.00[CEU][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs6137909	1.00[CEU][hapmap];0.82[MEX][hapmap];0.85[EUR][1000 genomes]
rs6137922	0.87[EUR][1000 genomes]
rs6137924	0.87[EUR][1000 genomes]
rs6137934	0.87[EUR][1000 genomes]
rs6137940	0.87[EUR][1000 genomes]
rs6137949	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7269627	0.85[EUR][1000 genomes]
rs743022	0.86[EUR][1000 genomes]
rs743023	1.00[CEU][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs743024	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs761724	0.80[AMR][1000 genomes]
rs761726	0.85[EUR][1000 genomes]
rs7988	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs8183442	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv912818	chr20:23406519-23567838	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv912819	chr20:23406519-23569400	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv912820	chr20:23406519-23578148	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1065390	chr20:23412890-23569238	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1065719	chr20:23415029-23565333	Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv544214	chr20:23415029-23565333	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2424557	CST9L	cis	parietal	SCAN
rs2424557	GINS1	cis	cerebellum	SCAN
rs2424557	NAPB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23417000-23422800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:23417200-23434800	Weak transcription	Gastric	stomach
3	chr20:23417600-23422400	Weak transcription	Brain Anterior Caudate	brain
4	chr20:23417800-23441000	Weak transcription	Right Atrium	heart
5	chr20:23421200-23427200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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