Variant report

Variant	rs420579
Chromosome Location	chr19:40564530-40564531
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	chr19:40561902..40564194-chr19:40564354..40569347,4	K562	blood:
2	chr19:40561268..40563176-chr19:40564032..40566450,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128000	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs1007628	0.94[ASN][1000 genomes]
rs10406738	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10417013	0.86[ASN][1000 genomes]
rs10417043	0.86[ASN][1000 genomes]
rs10418196	0.85[ASN][1000 genomes]
rs11542840	0.85[ASN][1000 genomes]
rs13344062	0.95[ASN][1000 genomes]
rs163213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973950	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs170900	0.85[ASN][1000 genomes]
rs170901	0.89[ASN][1000 genomes]
rs173061	0.86[ASN][1000 genomes]
rs17796769	0.85[ASN][1000 genomes]
rs17796901	0.89[ASN][1000 genomes]
rs183504	0.86[ASN][1000 genomes]
rs186801	0.86[ASN][1000 genomes]
rs186815	0.90[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1926931	0.89[ASN][1000 genomes]
rs1926932	0.89[ASN][1000 genomes]
rs1926933	0.89[ASN][1000 genomes]
rs1926934	0.89[ASN][1000 genomes]
rs2111543	0.86[ASN][1000 genomes]
rs2111544	0.86[ASN][1000 genomes]
rs2231737	0.85[ASN][1000 genomes]
rs234301	0.86[ASN][1000 genomes]
rs234302	0.89[ASN][1000 genomes]
rs234303	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234304	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234306	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234308	0.83[ASN][1000 genomes]
rs234309	0.86[ASN][1000 genomes]
rs234310	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234313	0.86[ASN][1000 genomes]
rs234315	0.86[ASN][1000 genomes]
rs234317	0.86[ASN][1000 genomes]
rs234318	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234323	0.86[ASN][1000 genomes]
rs234324	0.86[ASN][1000 genomes]
rs234325	0.86[ASN][1000 genomes]
rs234326	0.86[ASN][1000 genomes]
rs234328	0.86[ASN][1000 genomes]
rs234341	0.86[ASN][1000 genomes]
rs234343	0.90[ASN][1000 genomes]
rs234352	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234353	0.89[ASN][1000 genomes]
rs234355	0.89[ASN][1000 genomes]
rs234356	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234357	0.89[ASN][1000 genomes]
rs234360	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234361	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234370	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234371	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234374	0.86[ASN][1000 genomes]
rs2542303	0.86[ASN][1000 genomes]
rs2569650	0.80[ASN][1000 genomes]
rs2569651	0.81[ASN][1000 genomes]
rs2819956	0.86[ASN][1000 genomes]
rs28366011	0.86[ASN][1000 genomes]
rs2986595	0.89[ASN][1000 genomes]
rs3000956	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337779	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337780	0.85[ASN][1000 genomes]
rs337782	0.85[ASN][1000 genomes]
rs337798	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337799	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs337800	0.96[ASN][1000 genomes]
rs337801	0.93[ASN][1000 genomes]
rs365055	0.86[ASN][1000 genomes]
rs371500	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs372599	0.85[ASN][1000 genomes]
rs387202	0.86[ASN][1000 genomes]
rs392958	0.89[ASN][1000 genomes]
rs3930885	0.86[ASN][1000 genomes]
rs404754	0.86[ASN][1000 genomes]
rs416283	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421533	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423545	0.84[ASN][1000 genomes]
rs424353	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs426950	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577216	0.94[ASN][1000 genomes]
rs459091	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55798334	0.84[ASN][1000 genomes]
rs57219798	0.85[ASN][1000 genomes]
rs57880771	0.89[ASN][1000 genomes]
rs57900299	0.90[ASN][1000 genomes]
rs58210425	0.94[ASN][1000 genomes]
rs58284735	0.94[ASN][1000 genomes]
rs58395013	0.91[ASN][1000 genomes]
rs58440570	0.89[ASN][1000 genomes]
rs58941665	0.94[ASN][1000 genomes]
rs59502139	0.91[ASN][1000 genomes]
rs59925663	0.85[ASN][1000 genomes]
rs60080503	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60449727	0.90[ASN][1000 genomes]
rs60887294	0.86[ASN][1000 genomes]
rs61236589	0.86[ASN][1000 genomes]
rs61385499	0.89[ASN][1000 genomes]
rs615215	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247527	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7257747	0.90[ASN][1000 genomes]
rs7258202	0.90[ASN][1000 genomes]
rs7258506	0.91[ASN][1000 genomes]
rs7258627	0.91[ASN][1000 genomes]
rs7258778	0.90[ASN][1000 genomes]
rs7258974	0.89[ASN][1000 genomes]
rs7259855	0.89[ASN][1000 genomes]
rs7260378	0.89[ASN][1000 genomes]
rs73543974	0.85[ASN][1000 genomes]
rs73543979	0.85[ASN][1000 genomes]
rs73545909	0.86[ASN][1000 genomes]
rs73545911	0.86[ASN][1000 genomes]
rs73545934	0.86[ASN][1000 genomes]
rs73545936	0.86[ASN][1000 genomes]
rs73545938	0.86[ASN][1000 genomes]
rs73545945	0.86[ASN][1000 genomes]
rs73545950	0.86[ASN][1000 genomes]
rs73545955	0.86[ASN][1000 genomes]
rs73545975	0.86[ASN][1000 genomes]
rs73546001	0.86[ASN][1000 genomes]
rs73546002	0.86[ASN][1000 genomes]
rs73547618	0.86[ASN][1000 genomes]
rs73547620	0.86[ASN][1000 genomes]
rs73547638	0.86[ASN][1000 genomes]
rs73547652	0.89[ASN][1000 genomes]
rs73547656	0.89[ASN][1000 genomes]
rs73547663	0.89[ASN][1000 genomes]
rs73547676	0.89[ASN][1000 genomes]
rs73547677	0.89[ASN][1000 genomes]
rs73547696	0.94[ASN][1000 genomes]
rs73547702	0.94[ASN][1000 genomes]
rs73549804	0.91[ASN][1000 genomes]
rs73549810	0.91[ASN][1000 genomes]
rs73549811	0.91[ASN][1000 genomes]
rs73549820	0.91[ASN][1000 genomes]
rs73549821	0.85[ASN][1000 genomes]
rs73549825	0.89[ASN][1000 genomes]
rs73549826	0.89[ASN][1000 genomes]
rs73549829	0.89[ASN][1000 genomes]
rs73549833	0.89[ASN][1000 genomes]
rs73549835	0.89[ASN][1000 genomes]
rs73549836	0.89[ASN][1000 genomes]
rs8105066	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8106032	0.91[ASN][1000 genomes]
rs8108793	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783938	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9917073	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs420579	ZNF780A	cis	Esophagus Mucosa	GTEx
rs420579	ZNF780A	cis	lung	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40562600-40579200	Weak transcription	Left Ventricle	heart
2	chr19:40562600-40579400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:40563000-40565400	Weak transcription	Fetal Heart	heart
4	chr19:40563000-40565600	Weak transcription	Fetal Brain Male	brain
5	chr19:40563000-40565600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr19:40563200-40565600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:40563400-40566200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:40563600-40565600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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