Variant report

Variant	rs459091
Chromosome Location	chr19:40561175-40561176
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	chr19:40558581..40561504-chr19:40593898..40595454,2	K562	blood:
2	chr19:40475179..40477026-chr19:40560831..40562342,2	K562	blood:

Variant related genes	Relation type
ENSG00000013275	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:160)

rs_ID	r²[population]
rs1007628	0.92[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs10406738	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs170900	0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs170901	0.92[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs173061	0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs17796769	0.85[ASN][1000 genomes]
rs17796901	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs183504	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs186801	0.86[ASN][1000 genomes]
rs186815	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[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	0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2111544	0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2231737	0.92[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2231738	0.81[GIH][hapmap]
rs234301	0.88[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs234302	0.92[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs234303	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234304	1.00[CHB][hapmap];0.85[JPT][hapmap];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	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234323	0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs234324	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs234325	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs234326	0.86[ASN][1000 genomes]
rs234328	0.86[ASN][1000 genomes]
rs234341	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs234343	0.90[ASN][1000 genomes]
rs234352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234353	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs234355	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234370	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];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	0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs24136	0.80[CHD][hapmap]
rs2542303	0.86[ASN][1000 genomes]
rs2569650	0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs2569651	0.81[ASN][1000 genomes]
rs2767604	0.80[CHD][hapmap]
rs2819956	0.91[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs28366011	0.86[ASN][1000 genomes]
rs2915972	0.80[CHD][hapmap]
rs2986595	0.89[ASN][1000 genomes]
rs3000956	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];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]
rs337785	0.82[JPT][hapmap]
rs337789	0.80[CHD][hapmap]
rs337792	0.80[CHD][hapmap]
rs337794	0.82[JPT][hapmap]
rs337798	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337799	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs337800	0.96[ASN][1000 genomes]
rs337801	0.93[ASN][1000 genomes]
rs34466648	0.83[CHB][hapmap]
rs365055	0.86[ASN][1000 genomes]
rs371500	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs372599	0.85[ASN][1000 genomes]
rs3760919	0.85[GIH][hapmap]
rs3760920	0.83[CHB][hapmap]
rs387202	0.92[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs3887029	0.91[CHB][hapmap]
rs392958	0.92[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs3930885	0.86[ASN][1000 genomes]
rs404754	0.86[ASN][1000 genomes]
rs416283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577216	0.92[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.94[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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];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	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8106032	0.85[CEU][hapmap];0.92[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs8106269	0.88[GIH][hapmap]
rs8108793	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109718	0.88[GIH][hapmap]
rs9783938	0.93[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
rs459091	ZNF780A	cis	Esophagus Mucosa	GTEx
rs459091	ZNF780A	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40550000-40561200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:40552800-40561200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:40553000-40561400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:40553200-40561200	Weak transcription	HMEC	breast
5	chr19:40554400-40561200	Weak transcription	HUVEC	blood vessel
6	chr19:40554800-40561200	Weak transcription	HSMM	muscle
7	chr19:40554800-40561400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:40556800-40561200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:40556800-40561400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:40556800-40561400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:40556800-40561400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:40556800-40561400	Weak transcription	Esophagus	oesophagus
13	chr19:40556800-40561400	Weak transcription	Gastric	stomach
14	chr19:40557000-40561200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr19:40558000-40561200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:40558400-40561200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr19:40558400-40561200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:40559600-40561200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr19:40559800-40561200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr19:40559800-40561400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:40560200-40561600	Flanking Active TSS	Dnd41	blood
22	chr19:40560400-40561200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr19:40560400-40561200	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr19:40560400-40561200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:40560400-40561200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr19:40560400-40561600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr19:40560400-40561600	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr19:40560400-40561600	Flanking Active TSS	Fetal Brain Female	brain
29	chr19:40560400-40561800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr19:40560400-40562600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:40560400-40562600	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr19:40560400-40563000	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr19:40560400-40563000	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr19:40560400-40563000	Active TSS	Stomach Smooth Muscle	stomach
35	chr19:40560400-40563200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:40560600-40561200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:40560600-40561200	Enhancers	Brain Substantia Nigra	brain
38	chr19:40560600-40561200	Enhancers	Colonic Mucosa	Colon
39	chr19:40560600-40561200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr19:40560600-40561200	Flanking Active TSS	Fetal Heart	heart
41	chr19:40560600-40561200	Enhancers	Fetal Muscle Leg	muscle
42	chr19:40560600-40561200	Enhancers	Ovary	ovary
43	chr19:40560600-40561200	Enhancers	NHEK	skin
44	chr19:40560600-40561400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr19:40560600-40561400	Enhancers	Primary B cells from peripheral blood	blood
46	chr19:40560600-40561400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:40560600-40561400	Flanking Active TSS	Brain Germinal Matrix	brain
48	chr19:40560600-40561400	Flanking Active TSS	Fetal Brain Male	brain
49	chr19:40560600-40561400	Enhancers	Pancreas	Pancrea
50	chr19:40560600-40561400	Enhancers	Stomach Mucosa	stomach

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