Variant report

Variant	rs421533
Chromosome Location	chr19:40579468-40579469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40577512..40581181-chr19:40595512..40598520,4	K562	blood:
2	chr19:40574294..40577886-chr19:40578085..40580406,4	K562	blood:
3	chr19:40561659..40563335-chr19:40578220..40580556,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197782	Chromatin interaction
ENSG00000269296	Chromatin interaction
ENSG00000128000	Chromatin interaction
ENSG00000269749	Chromatin interaction

Extended variants
information (count: 175 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:173)

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];0.81[YRI][hapmap];0.84[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]
rs1327185	0.85[JPT][hapmap]
rs1327193	0.82[JPT][hapmap]
rs13344062	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs163213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[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];0.83[YRI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16974093	0.80[AFR][1000 genomes]
rs170900	0.87[CHD][hapmap];0.85[ASN][1000 genomes]
rs170901	0.92[CHB][hapmap];1.00[JPT][hapmap];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];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17797100	0.85[JPT][hapmap]
rs183504	0.92[CHB][hapmap];0.93[CHD][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[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]
rs2231738	0.81[GIH][hapmap]
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	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234306	0.87[YRI][hapmap];0.84[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];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs234310	0.84[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];0.81[YRI][hapmap];0.84[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];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs234325	0.92[CHB][hapmap];0.93[CHD][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];0.93[CHD][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];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs234353	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs234355	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs234356	0.84[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];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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234371	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs234374	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs24135	0.85[JPT][hapmap]
rs24136	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs24137	0.85[JPT][hapmap]
rs2542303	0.86[ASN][1000 genomes]
rs2569640	0.85[JPT][hapmap]
rs2569641	0.85[JPT][hapmap]
rs2569650	0.94[ASW][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2569651	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2767604	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs2767607	0.85[JPT][hapmap]
rs2819956	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs28366011	0.86[ASN][1000 genomes]
rs2915972	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs2986595	0.89[ASN][1000 genomes]
rs3000956	0.88[AFR][1000 genomes];0.95[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];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[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]
rs337784	0.85[JPT][hapmap]
rs337785	1.00[JPT][hapmap]
rs337786	0.85[JPT][hapmap]
rs337787	0.84[JPT][hapmap]
rs337789	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs337792	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs337793	0.85[JPT][hapmap]
rs337794	1.00[JPT][hapmap]
rs337798	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.97[ASN][1000 genomes]
rs337800	0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs337801	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs34466648	0.83[CHB][hapmap]
rs365055	0.86[ASN][1000 genomes]
rs371500	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.81[YRI][hapmap];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];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3887029	0.91[CHB][hapmap]
rs392958	0.92[CHB][hapmap];1.00[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[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420579	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs423545	0.84[ASN][1000 genomes]
rs424353	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs426950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[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]
rs4577216	0.92[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs459091	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]
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	0.84[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[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8106032	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs8106269	0.88[GIH][hapmap]
rs8108793	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109718	0.88[GIH][hapmap]
rs9783938	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9917073	0.84[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs421533	ZNF780A	cis	Esophagus Mucosa	GTEx
rs421533	ZNF780A	cis	lung	GTEx
rs421533	AC005614.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40566000-40580000	Weak transcription	Fetal Heart	heart
2	chr19:40570600-40579800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr19:40571800-40579600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:40572400-40579600	Weak transcription	Ovary	ovary
5	chr19:40572400-40580000	Weak transcription	Lung	lung
6	chr19:40572400-40580000	Weak transcription	Pancreas	Pancrea
7	chr19:40573000-40580000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr19:40573800-40580000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr19:40574000-40580000	Weak transcription	Right Ventricle	heart
10	chr19:40574400-40580000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:40574400-40582400	Weak transcription	Fetal Stomach	stomach
12	chr19:40574800-40580000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:40575200-40579600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr19:40575200-40580000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:40575400-40580200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:40575600-40579800	Weak transcription	Colon Smooth Muscle	Colon
17	chr19:40575800-40579800	Weak transcription	Small Intestine	intestine
18	chr19:40576800-40579800	Weak transcription	Fetal Brain Male	brain
19	chr19:40577000-40579800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:40577000-40580000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr19:40577200-40579600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr19:40577200-40579600	Weak transcription	Brain Substantia Nigra	brain
23	chr19:40577200-40579800	Weak transcription	Fetal Intestine Large	intestine
24	chr19:40577400-40579600	Weak transcription	Brain Anterior Caudate	brain
25	chr19:40577600-40579800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:40578000-40579600	Weak transcription	Brain Hippocampus Middle	brain
27	chr19:40578000-40579600	Weak transcription	Fetal Thymus	thymus
28	chr19:40578000-40579800	Weak transcription	Brain Angular Gyrus	brain
29	chr19:40578200-40579800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr19:40578200-40580000	Weak transcription	Placenta	Placenta
31	chr19:40578400-40580200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:40578400-40580200	Weak transcription	NHDF-Ad	bronchial
33	chr19:40578600-40579800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr19:40578600-40580000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:40578600-40580200	Weak transcription	Gastric	stomach
36	chr19:40578600-40586200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
37	chr19:40578600-40586600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:40578600-40586600	ZNF genes & repeats	Liver	Liver
39	chr19:40578600-40586600	ZNF genes & repeats	A549	lung
40	chr19:40578600-40586800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:40578600-40590400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:40578800-40579800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr19:40578800-40579800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr19:40578800-40579800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr19:40578800-40580200	Strong transcription	Brain Germinal Matrix	brain
46	chr19:40578800-40581000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:40578800-40582000	Strong transcription	Dnd41	blood
48	chr19:40578800-40582400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:40578800-40582600	Strong transcription	Colonic Mucosa	Colon
50	chr19:40578800-40583600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood

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