Variant report

Variant	rs416283
Chromosome Location	chr19:40550956-40550957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 153 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs1007628	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10406738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs170900	0.85[ASN][1000 genomes]
rs170901	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs173061	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17796769	0.85[ASN][1000 genomes]
rs17796901	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs183504	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs186801	0.86[ASN][1000 genomes]
rs186815	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2111544	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2231737	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs234301	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs234302	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs234303	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234304	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234306	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234308	0.83[ASN][1000 genomes]
rs234309	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs234310	1.00[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];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234323	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs234324	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs234325	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs234326	0.86[ASN][1000 genomes]
rs234328	0.86[ASN][1000 genomes]
rs234341	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs234343	0.90[ASN][1000 genomes]
rs234352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234353	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs234355	0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs234356	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234357	0.87[AMR][1000 genomes];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];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234371	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234374	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2542303	0.86[ASN][1000 genomes]
rs2569650	0.80[ASN][1000 genomes]
rs2569651	0.81[ASN][1000 genomes]
rs2819956	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28366011	0.86[ASN][1000 genomes]
rs2986595	0.89[ASN][1000 genomes]
rs3000956	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[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	1.00[JPT][hapmap]
rs337794	1.00[JPT][hapmap]
rs337798	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337799	1.00[CHB][hapmap];1.00[JPT][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	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs372599	0.85[ASN][1000 genomes]
rs3760920	0.83[CHB][hapmap]
rs387202	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3887029	0.91[CHB][hapmap]
rs392958	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3930885	0.86[ASN][1000 genomes]
rs404754	0.86[ASN][1000 genomes]
rs420579	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs421533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423545	0.84[ASN][1000 genomes]
rs424353	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs426950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs4577216	0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs459091	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]
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	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8106032	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8108793	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783938	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9917073	1.00[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
rs416283	ZNF780A	cis	lung	GTEx
rs416283	ZNF780A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40548400-40552400	Weak transcription	Hela-S3	cervix
2	chr19:40549000-40551200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
3	chr19:40549000-40551800	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:40549000-40553200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
5	chr19:40549000-40553200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr19:40549000-40553400	ZNF genes & repeats	Fetal Lung	lung
7	chr19:40549000-40554200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:40549000-40554800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
9	chr19:40549000-40556800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
10	chr19:40549000-40556800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:40549000-40559800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:40549200-40551000	Strong transcription	Psoas Muscle	Psoas
13	chr19:40549200-40551200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:40549200-40551200	ZNF genes & repeats	Brain Anterior Caudate	brain
15	chr19:40549200-40551400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:40549200-40551400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
17	chr19:40549200-40551600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
18	chr19:40549200-40552000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:40549200-40552600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
20	chr19:40549200-40552800	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
21	chr19:40549200-40552800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr19:40549200-40552800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:40549200-40553000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:40549200-40553200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
25	chr19:40549200-40553400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
26	chr19:40549200-40553800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr19:40549200-40555200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr19:40549200-40555800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:40549200-40556400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:40549200-40556800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:40549200-40556800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:40549200-40556800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr19:40549200-40556800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:40549200-40556800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:40549200-40556800	ZNF genes & repeats	Brain Germinal Matrix	brain
36	chr19:40549200-40556800	ZNF genes & repeats	Fetal Brain Female	brain
37	chr19:40549200-40556800	ZNF genes & repeats	Fetal Kidney	kidney
38	chr19:40549200-40556800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
39	chr19:40549200-40557800	ZNF genes & repeats	Liver	Liver
40	chr19:40549400-40551200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
41	chr19:40549400-40551400	ZNF genes & repeats	Primary B cells from cord blood	blood
42	chr19:40549400-40551400	ZNF genes & repeats	Brain Substantia Nigra	brain
43	chr19:40549400-40551600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
44	chr19:40549400-40552400	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr19:40549400-40552800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
46	chr19:40549400-40552800	ZNF genes & repeats	Colon Smooth Muscle	Colon
47	chr19:40549400-40552800	ZNF genes & repeats	Dnd41	blood
48	chr19:40549400-40553000	ZNF genes & repeats	Primary T cells from cord blood	blood
49	chr19:40549400-40553000	ZNF genes & repeats	Fetal Intestine Large	intestine
50	chr19:40549400-40553000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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