Variant report

Variant	rs2039398
Chromosome Location	chr1:155538579-155538580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155535397..155538266-chr1:155538326..155540106,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271267	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12730906	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34201109	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34228238	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35212551	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35264597	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36035038	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71517783	0.84[EUR][1000 genomes]
rs71628672	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs71628683	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628688	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv872468	chr1:155413304-155549562	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	esv3431739	chr1:155514331-155664183	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription 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	61 gene(s)	inside rSNPs	diseases
6	esv3388968	chr1:155532335-155658278	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2039398	GBA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155533400-155549000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:155534000-155539400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:155534200-155542800	Weak transcription	Esophagus	oesophagus
4	chr1:155534200-155543000	Weak transcription	Brain Germinal Matrix	brain
5	chr1:155534200-155547600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:155534400-155540000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:155534400-155544200	Weak transcription	Fetal Brain Female	brain
8	chr1:155534600-155539200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr1:155534600-155539800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:155534600-155539800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:155534600-155539800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:155534600-155539800	Weak transcription	Fetal Heart	heart
13	chr1:155534600-155539800	Weak transcription	NH-A	brain
14	chr1:155534600-155540000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:155534600-155540000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:155534600-155540000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:155534600-155540200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:155534600-155542000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:155534600-155542000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:155534600-155542000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:155534600-155542200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:155534600-155542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:155534600-155542400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:155534600-155542400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:155534600-155543000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:155534600-155543000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:155534600-155560400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:155534600-155565800	Weak transcription	Brain Hippocampus Middle	brain
29	chr1:155534800-155539400	Weak transcription	Primary T cells from cord blood	blood
30	chr1:155534800-155539800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:155534800-155539800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr1:155534800-155540000	Weak transcription	Spleen	Spleen
33	chr1:155534800-155540200	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:155534800-155540200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr1:155534800-155540200	Weak transcription	Left Ventricle	heart
36	chr1:155534800-155540800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:155534800-155541000	Weak transcription	HSMMtube	muscle
38	chr1:155534800-155542200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:155534800-155542600	Weak transcription	NHLF	lung
40	chr1:155534800-155543000	Weak transcription	HepG2	liver
41	chr1:155534800-155543200	Weak transcription	Pancreas	Pancrea
42	chr1:155534800-155544800	Weak transcription	Brain Anterior Caudate	brain
43	chr1:155534800-155558200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:155534800-155561800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr1:155534800-155565600	Weak transcription	Brain Angular Gyrus	brain
46	chr1:155534800-155568400	Weak transcription	Thymus	Thymus
47	chr1:155535000-155539800	Weak transcription	Fetal Intestine Large	intestine
48	chr1:155535000-155541000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:155535000-155541800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:155535000-155543200	Weak transcription	Rectal Mucosa Donor 29	rectum

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