Variant report

Variant	rs3803917
Chromosome Location	chr19:18669883-18669884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr19:18669026-18669923	GM12878	blood:	n/a	n/a
2	ZNF384	chr19:18669578-18669939	K562	blood:	n/a	n/a
3	POLR2A	chr19:18669850-18669886	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:18667793-18670191	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:18668110-18669945	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:18669347-18670103	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:18668145-18669883	K562	blood:	n/a	n/a
8	RCOR1	chr19:18667650-18669920	IMR90	lung:	n/a	n/a
9	ESRRA	chr19:18668009-18669888	GM12878	blood:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18652388..18654838-chr19:18668474..18670630,2	K562	blood:
2	chr19:18631459..18633367-chr19:18667345..18670376,4	K562	blood:
3	chr19:18546792..18548978-chr19:18667741..18669982,2	K562	blood:
4	chr19:18669154..18672917-chr19:18697910..18700793,4	K562	blood:
5	chr19:18630485..18634839-chr19:18666846..18671916,7	MCF-7	breast:
6	chr19:18652388..18655450-chr19:18667016..18670630,4	K562	blood:
7	chr19:18643154..18644865-chr19:18669645..18671230,2	K562	blood:
8	chr19:18666812..18670172-chr19:18680715..18684041,6	MCF-7	breast:
9	chr19:18653032..18656930-chr19:18667045..18670995,8	MCF-7	breast:
10	chr19:18630548..18633267-chr19:18667345..18670044,3	K562	blood:
11	chr19:18667424..18670168-chr19:18699281..18701481,3	MCF-7	breast:
12	chr19:18653886..18656782-chr19:18668675..18670368,2	MCF-7	breast:
13	chr19:18667097..18671007-chr19:18677068..18684435,17	K562	blood:
14	chr19:18649378..18653671-chr19:18667425..18670328,5	MCF-7	breast:
15	chr19:18392874..18395450-chr19:18668198..18669959,2	K562	blood:
16	chr19:18667740..18670829-chr19:18672165..18676171,4	K562	blood:
17	chr19:18666965..18674770-chr19:18676405..18685095,25	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FKBP8-1	chr19:18668585-18670453	ENSG00000268030.1

No data

Variant related genes	Relation type
KXD1	TF binding region
ENSG00000221983	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000268030	Chromatin interaction
ENSG00000267959	Chromatin interaction
ENSG00000268983	Chromatin interaction
ENSG00000105655	Chromatin interaction
ENSG00000105701	Chromatin interaction
ENSG00000105700	Chromatin interaction
ENSG00000269191	Chromatin interaction
ENSG00000105656	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10402321	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10414427	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10425018	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11086114	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11086116	0.87[ASN][1000 genomes]
rs11667551	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11672297	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12150991	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12608925	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12609505	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1468475	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2057649	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2058077	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2079015	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2079016	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2283616	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2302055	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2314664	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2314665	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2314666	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2314667	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28451415	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28711754	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28884574	0.85[ASN][1000 genomes]
rs35867875	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35875334	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36050418	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3761034	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3761036	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4629093	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4808137	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808821	0.82[ASN][1000 genomes]
rs55724121	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55888366	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58782998	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59798925	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62137086	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7247557	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7253088	0.83[ASN][1000 genomes]
rs7254004	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7258480	0.81[ASN][1000 genomes]
rs7648	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8110371	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110374	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911274	chr19:18440942-18691942	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv1061733	chr19:18574940-18679155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1055794	chr19:18611545-18676933	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv911283	chr19:18626732-18689830	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv911284	chr19:18643036-18684216	Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
12	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
13	esv3417112	chr19:18669858-18670380	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3803917	UBA52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18668200-18670000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr19:18668400-18670200	Active TSS	GM12878-XiMat	blood
3	chr19:18669200-18670200	Flanking Active TSS	NHEK	skin
4	chr19:18669400-18670000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:18669400-18670000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:18669400-18670000	Enhancers	Spleen	Spleen
7	chr19:18669400-18670000	Flanking Active TSS	NHLF	lung
8	chr19:18669400-18670200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:18669400-18670600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:18669400-18670600	Flanking Active TSS	Dnd41	blood
11	chr19:18669400-18672400	Weak transcription	Ovary	ovary
12	chr19:18669400-18675600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:18669600-18670000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr19:18669600-18670000	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr19:18669600-18670000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr19:18669600-18670000	Enhancers	Fetal Muscle Leg	muscle
17	chr19:18669600-18670000	Enhancers	Right Ventricle	heart
18	chr19:18669600-18670200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:18669600-18670400	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr19:18669600-18670400	Enhancers	Brain Anterior Caudate	brain
21	chr19:18669600-18670400	Enhancers	Stomach Mucosa	stomach
22	chr19:18669600-18670600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:18669600-18670600	Enhancers	Primary B cells from cord blood	blood
24	chr19:18669600-18670600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr19:18669600-18670600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr19:18669600-18670600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:18669600-18670600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr19:18669600-18670600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:18669600-18670600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr19:18669600-18670600	Enhancers	Brain Cingulate Gyrus	brain
31	chr19:18669600-18670800	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr19:18669600-18670800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:18669600-18670800	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr19:18669600-18671200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr19:18669600-18672400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr19:18669600-18672400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr19:18669600-18672400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:18669600-18672400	Weak transcription	Fetal Lung	lung
39	chr19:18669600-18672400	Weak transcription	Gastric	stomach
40	chr19:18669600-18674800	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:18669600-18675400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr19:18669600-18675400	Weak transcription	Fetal Kidney	kidney
43	chr19:18669600-18677600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr19:18669800-18670000	Enhancers	Psoas Muscle	Psoas
45	chr19:18669800-18670000	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr19:18669800-18670000	Weak transcription	A549	lung
47	chr19:18669800-18670000	Enhancers	HSMM	muscle
48	chr19:18669800-18670000	Enhancers	HUVEC	blood vessel
49	chr19:18669800-18670000	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr19:18669800-18670200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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