Variant report

Variant	rs3754485
Chromosome Location	chr1:155212211-155212212
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155211622..155214565-chr1:155278095..155280494,4	MCF-7	breast:
2	chr1:155161998..155164147-chr1:155209813..155212664,2	K562	blood:
3	chr1:155176876..155179171-chr1:155209871..155213021,3	K562	blood:
4	chr1:155187157..155191331-chr1:155209670..155212928,5	MCF-7	breast:
5	chr1:155174858..155180302-chr1:155209102..155215747,8	MCF-7	breast:
6	chr1:155176431..155180791-chr1:155209413..155214573,7	MCF-7	breast:
7	chr1:155211806..155213841-chr1:155274140..155275790,2	K562	blood:
8	chr1:155209727..155212678-chr1:155212773..155217086,5	K562	blood:
9	chr1:155212049..155215843-chr1:155293307..155296856,5	MCF-7	breast:
10	chr1:155200890..155203810-chr1:155211180..155212788,2	MCF-7	breast:
11	chr1:154973468..154975172-chr1:155209592..155212426,2	MCF-7	breast:
12	chr1:155211725..155212274-chr1:155294201..155294747,2	Hela-S3	cervix:
13	chr1:155176699..155181010-chr1:155210436..155216018,7	K562	blood:
14	chr1:155210404..155213133-chr1:155222950..155225276,2	MCF-7	breast:
15	chr1:155209487..155212728-chr1:155212760..155217156,9	MCF-7	breast:
16	chr1:155211497..155213419-chr17:60004081..60005775,2	MCF-7	breast:
17	chr1:155195600..155203152-chr1:155209955..155216515,9	MCF-7	breast:
18	chr1:155195599..155199380-chr1:155211353..155216703,7	MCF-7	breast:
19	chr1:155161998..155167332-chr1:155208163..155212538,6	K562	blood:
20	chr1:155195406..155199356-chr1:155210414..155216260,10	K562	blood:
21	chr1:155193188..155195403-chr1:155211959..155214156,2	K562	blood:
22	chr1:155207800..155212678-chr1:155214121..155217855,6	K562	blood:
23	chr1:155209079..155212795-chr1:155212935..155216540,4	MCF-7	breast:
24	chr1:155211690..155216212-chr1:155231766..155235735,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225855	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000173171	Chromatin interaction
ENSG00000160685	Chromatin interaction
ENSG00000271748	Chromatin interaction
ENSG00000108506	Chromatin interaction
ENSG00000231064	Chromatin interaction
ENSG00000160753	Chromatin interaction
ENSG00000177628	Chromatin interaction
ENSG00000160752	Chromatin interaction
ENSG00000116521	Chromatin interaction
ENSG00000160767	Chromatin interaction
ENSG00000236675	Chromatin interaction
ENSG00000160766	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1045253	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1046188	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1052176	0.82[ASN][1000 genomes]
rs1052177	0.82[ASN][1000 genomes]
rs1076556	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1078699	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10796940	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908459	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264343	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264345	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264346	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11264348	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11264349	0.83[ASN][1000 genomes]
rs11264352	0.85[ASN][1000 genomes]
rs11264353	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1142287	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11577338	0.86[ASN][1000 genomes]
rs12034326	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12042020	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12044063	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12049375	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12406363	0.84[ASN][1000 genomes]
rs12407919	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12411216	0.81[AFR][1000 genomes]
rs12563994	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12723761	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12724449	0.85[ASN][1000 genomes]
rs12748155	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12749306	0.85[ASN][1000 genomes]
rs1546818	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1800438	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800442	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807042	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2009578	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049805	0.90[AFR][1000 genomes]
rs2066981	0.85[AFR][1000 genomes]
rs2071053	0.82[ASN][1000 genomes]
rs2072647	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2075566	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2075569	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075570	0.87[AFR][1000 genomes]
rs2236863	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2236864	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2242576	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2242577	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2361536	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2361543	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs28373017	0.92[ASN][1000 genomes]
rs28445596	0.89[AFR][1000 genomes]
rs28595322	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2974929	0.88[AFR][1000 genomes]
rs2974930	0.89[AFR][1000 genomes]
rs2974931	0.88[AFR][1000 genomes]
rs2974935	0.87[AFR][1000 genomes]
rs2974937	0.85[AFR][1000 genomes]
rs2990220	0.86[AFR][1000 genomes]
rs2990245	0.88[AFR][1000 genomes]
rs370545	0.84[AFR][1000 genomes]
rs3768566	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3814318	0.80[ASN][1000 genomes]
rs3814319	0.82[ASN][1000 genomes]
rs4043	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4620533	0.82[ASN][1000 genomes]
rs497829	0.90[AFR][1000 genomes]
rs56310840	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59352002	0.84[AMR][1000 genomes]
rs734073	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs734074	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs741756	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7520184	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7543234	0.81[AMR][1000 genomes]
rs7549276	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7554780	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs760077	0.81[AFR][1000 genomes]
rs762488	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8847	0.82[ASN][1000 genomes]
rs914615	0.85[AFR][1000 genomes]
rs932972	0.82[ASN][1000 genomes]
rs9628662	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9729564	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
4	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
5	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
6	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
7	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
8	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
9	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
10	nsv870053	chr1:155180349-155212316	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
11	esv13606	chr1:155180489-155221243	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
12	nsv1008748	chr1:155189148-155230610	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
13	nsv1011773	chr1:155189148-155234821	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
14	esv1793876	chr1:155194112-155212255	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
15	nsv8480	chr1:155206335-155214536	Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	diseases
16	nsv947198	chr1:155206997-155226440	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3754485	GBA	cis	Esophagus Mucosa	GTEx
rs3754485	GBAP1	cis	Esophagus Mucosa	GTEx
rs3754485	GBA	cis	Whole Blood	GTEx
rs3754485	RP11-263K19.4	cis	Whole Blood	GTEx
rs3754485	GBAP1	cis	Thyroid	GTEx
rs3754485	THBS3	cis	Whole Blood	GTEx
rs3754485	GBAP1	cis	Artery Tibial	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155197200-155212800	Weak transcription	Small Intestine	intestine
2	chr1:155208000-155213000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:155210000-155213400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:155210600-155213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:155211000-155213400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:155211000-155214200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr1:155211200-155212800	Enhancers	NHLF	lung
8	chr1:155211200-155213000	Enhancers	Fetal Muscle Leg	muscle
9	chr1:155211200-155213000	Enhancers	Fetal Thymus	thymus
10	chr1:155211200-155213000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr1:155211200-155213000	Weak transcription	HSMMtube	muscle
12	chr1:155211200-155213000	Enhancers	HUVEC	blood vessel
13	chr1:155211200-155213200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:155211200-155213200	Enhancers	Primary T cells from cord blood	blood
15	chr1:155211200-155213200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:155211200-155213200	Weak transcription	Right Atrium	heart
17	chr1:155211200-155213400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr1:155211200-155213400	Enhancers	Placenta	Placenta
19	chr1:155211200-155213600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:155211200-155213600	Weak transcription	Ovary	ovary
21	chr1:155211200-155213800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:155211400-155212600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:155211400-155212800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:155211400-155212800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:155211400-155213000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:155211400-155213000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:155211400-155213000	Enhancers	Adipose Nuclei	Adipose
28	chr1:155211400-155213000	Weak transcription	Brain Germinal Matrix	brain
29	chr1:155211400-155213000	Enhancers	Colon Smooth Muscle	Colon
30	chr1:155211400-155213000	Weak transcription	Fetal Intestine Large	intestine
31	chr1:155211400-155213000	Weak transcription	Fetal Lung	lung
32	chr1:155211400-155213000	Weak transcription	Fetal Stomach	stomach
33	chr1:155211400-155213000	Enhancers	Thymus	Thymus
34	chr1:155211400-155213200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:155211400-155213200	Weak transcription	Aorta	Aorta
36	chr1:155211400-155213200	Enhancers	Duodenum Mucosa	Duodenum
37	chr1:155211400-155213200	Weak transcription	Fetal Kidney	kidney
38	chr1:155211400-155213200	Weak transcription	Psoas Muscle	Psoas
39	chr1:155211400-155213200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr1:155211400-155213400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr1:155211600-155212600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:155211600-155212600	Enhancers	NHDF-Ad	bronchial
43	chr1:155211600-155212800	Weak transcription	Brain Substantia Nigra	brain
44	chr1:155211600-155212800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:155211600-155212800	Weak transcription	A549	lung
46	chr1:155211600-155213000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:155211600-155213000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:155211600-155213000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:155211600-155213000	Weak transcription	Brain Angular Gyrus	brain
50	chr1:155211600-155213000	Weak transcription	Brain Cingulate Gyrus	brain

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