Variant report

Variant	rs7258480
Chromosome Location	chr19:18692666-18692667
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18690220..18695010-chr19:18697140..18702125,7	MCF-7	breast:
2	chr19:18624925..18627602-chr19:18688802..18692839,3	K562	blood:
3	chr19:18685970..18689439-chr19:18690944..18695066,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006015	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10425018	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11667551	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12150991	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12608925	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12609505	0.82[ASN][1000 genomes]
rs1468475	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2057649	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2058077	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2079015	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2079016	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2283616	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2302055	0.87[ASN][1000 genomes]
rs2314664	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2314665	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2314666	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2314667	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28451415	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28711754	0.84[ASN][1000 genomes]
rs35867875	0.87[ASN][1000 genomes]
rs35875334	0.87[ASN][1000 genomes]
rs36050418	0.80[ASN][1000 genomes]
rs3761034	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3761036	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3803917	0.81[ASN][1000 genomes]
rs4629093	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808137	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55888366	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58782998	0.84[ASN][1000 genomes]
rs62137086	0.87[ASN][1000 genomes]
rs6554	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7253088	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7254004	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7648	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7258480	UBA52	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18684400-18698600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:18684600-18698800	Weak transcription	Right Atrium	heart
3	chr19:18686200-18698600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:18686800-18698400	Weak transcription	Colonic Mucosa	Colon
5	chr19:18686800-18699600	Weak transcription	Small Intestine	intestine
6	chr19:18687000-18698600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:18687200-18693200	Weak transcription	K562	blood
8	chr19:18687200-18693200	Weak transcription	NHDF-Ad	bronchial
9	chr19:18687200-18698600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:18687200-18698800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr19:18687200-18698800	Weak transcription	HSMMtube	muscle
12	chr19:18687200-18699000	Weak transcription	Aorta	Aorta
13	chr19:18687200-18699400	Weak transcription	Ovary	ovary
14	chr19:18687400-18696200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:18687400-18696200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:18687400-18696400	Weak transcription	Primary B cells from cord blood	blood
17	chr19:18687400-18698600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr19:18687400-18698600	Weak transcription	Fetal Lung	lung
19	chr19:18687400-18698600	Weak transcription	Hela-S3	cervix
20	chr19:18687400-18698800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:18687400-18698800	Weak transcription	Psoas Muscle	Psoas
22	chr19:18687400-18699000	Weak transcription	Brain Substantia Nigra	brain
23	chr19:18687600-18695200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:18687600-18698600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:18687600-18698600	Weak transcription	HSMM	muscle
26	chr19:18687600-18698800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:18687800-18696200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr19:18687800-18698600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr19:18687800-18698800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:18687800-18698800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr19:18687800-18699000	Weak transcription	Pancreas	Pancrea
32	chr19:18688000-18698600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:18688000-18698800	Weak transcription	Fetal Kidney	kidney
34	chr19:18688200-18696200	Weak transcription	Dnd41	blood
35	chr19:18688200-18698600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:18688200-18698800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr19:18688400-18692800	Weak transcription	Fetal Intestine Large	intestine
38	chr19:18688400-18696000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:18688400-18698600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:18688400-18698600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr19:18688400-18699000	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:18688600-18695000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr19:18688600-18696000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr19:18688600-18697800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:18688600-18698400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:18688600-18698600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:18688600-18698800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr19:18688600-18699000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr19:18688600-18699000	Weak transcription	A549	lung
50	chr19:18688800-18693200	Weak transcription	Brain Germinal Matrix	brain

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