Variant report

Variant	rs6509139
Chromosome Location	chr19:44583103-44583104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11083736	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11083737	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11666432	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12610472	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1474061	0.81[EUR][1000 genomes]
rs2138823	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2138824	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2176431	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3826941	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4239528	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4299256	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4371266	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4375771	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4444434	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4550576	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4555257	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803668	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803672	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4803674	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55798868	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56003307	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56230322	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56250154	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57895932	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62115491	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62119177	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6509135	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6509137	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7251015	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7252213	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7255192	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8105003	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8109313	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8109615	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8110348	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9646633	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6509139	ZNF223	cis	Skin Sun Exposed Lower leg	GTEx
rs6509139	ZNF223	cis	lung	GTEx
rs6509139	ZNF223	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44577000-44585000	Weak transcription	Pancreas	Pancrea
2	chr19:44577000-44598000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:44577200-44584200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:44577200-44584800	Weak transcription	Right Ventricle	heart
5	chr19:44577200-44585000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:44577200-44585000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:44577200-44585000	Weak transcription	Colonic Mucosa	Colon
8	chr19:44577200-44585000	Weak transcription	Esophagus	oesophagus
9	chr19:44577200-44586200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:44577200-44586200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:44577200-44586200	Weak transcription	HUVEC	blood vessel
12	chr19:44577200-44588000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr19:44577200-44588200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:44577200-44590000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:44577200-44598000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:44577400-44584200	Weak transcription	Aorta	Aorta
17	chr19:44577400-44584200	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:44577400-44584200	Weak transcription	Fetal Thymus	thymus
19	chr19:44577400-44584200	Weak transcription	Ovary	ovary
20	chr19:44577400-44584200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:44577400-44584200	Weak transcription	Spleen	Spleen
22	chr19:44577400-44584800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr19:44577400-44584800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:44577400-44584800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr19:44577400-44584800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:44577400-44584800	Weak transcription	Brain Angular Gyrus	brain
27	chr19:44577400-44584800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr19:44577400-44584800	Weak transcription	Brain Hippocampus Middle	brain
29	chr19:44577400-44585000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:44577400-44585000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr19:44577400-44585000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:44577400-44585000	Weak transcription	Small Intestine	intestine
33	chr19:44577400-44585200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:44577400-44586200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:44577400-44586400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr19:44577400-44589200	Weak transcription	NH-A	brain
37	chr19:44577600-44584000	Weak transcription	Adipose Nuclei	Adipose
38	chr19:44577600-44584200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:44577600-44584200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:44577600-44584200	Weak transcription	Brain Germinal Matrix	brain
41	chr19:44577600-44584200	Weak transcription	NHLF	lung
42	chr19:44577600-44584800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr19:44577600-44584800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:44577600-44584800	Weak transcription	Brain Anterior Caudate	brain
45	chr19:44577600-44584800	Weak transcription	Brain Substantia Nigra	brain
46	chr19:44577600-44584800	Weak transcription	Placenta	Placenta
47	chr19:44577600-44584800	Weak transcription	Thymus	Thymus
48	chr19:44577600-44584800	Weak transcription	HSMMtube	muscle
49	chr19:44577600-44585000	Weak transcription	Gastric	stomach
50	chr19:44577600-44585000	Weak transcription	Psoas Muscle	Psoas

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