Variant report

Variant	rs10908461
Chromosome Location	chr1:155275727-155275728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr1:155275721-155275963	GM12878	blood:	n/a	chr1:155275801-155275810 chr1:155275801-155275810 chr1:155275799-155275812 chr1:155275799-155275810
2	HEY1	chr1:155275068-155275990	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155270303..155273300-chr1:155273424..155278245,4	MCF-7	breast:
2	chr1:155275443..155277458-chr1:155656857..155658578,2	K562	blood:
3	chr1:155254134..155256609-chr1:155273480..155276250,2	MCF-7	breast:
4	chr1:155211806..155213841-chr1:155274140..155275790,2	K562	blood:
5	chr1:155231272..155233234-chr1:155274983..155276852,2	MCF-7	breast:
6	chr1:155146607..155148418-chr1:155274675..155276271,2	K562	blood:
7	chr1:155246042..155249168-chr1:155274467..155279979,9	MCF-7	breast:
8	chr1:155245770..155249042-chr1:155274997..155278484,6	K562	blood:
9	chr1:155274938..155276540-chr1:155276885..155279319,2	K562	blood:

Variant related genes	Relation type
PKLR	TF binding region
FDPS	TF binding region
ENSG00000176444	Chromatin interaction
ENSG00000160752	Chromatin interaction
ENSG00000163462	Chromatin interaction
ENSG00000143627	Chromatin interaction
ENSG00000116521	Chromatin interaction
ENSG00000143630	Chromatin interaction
ENSG00000132676	Chromatin interaction
ENSG00000163374	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1052176	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1052177	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10796941	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10908462	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10908463	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264349	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11264352	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11264353	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11264354	0.86[EUR][1000 genomes]
rs11264355	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11264357	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264358	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264359	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264360	0.82[AMR][1000 genomes]
rs11264361	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12032720	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044063	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12049375	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12067675	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12563994	0.81[ASN][1000 genomes]
rs12724449	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12749306	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2071053	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236863	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2297480	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2361543	0.80[AMR][1000 genomes]
rs3020781	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3814318	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3814319	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4620533	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971072	0.99[ASN][1000 genomes]
rs6672284	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7520184	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7524950	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7534795	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549276	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7554780	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8177968	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8847	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs932972	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[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	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
2	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
3	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
4	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
5	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
6	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	67 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10908461	GBA	cis	Esophagus Mucosa	GTEx
rs10908461	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs10908461	PKLR	cis	Nerve Tibial	GTEx
rs10908461	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs10908461	GBAP1	cis	Artery Tibial	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155265400-155277800	Weak transcription	Right Atrium	heart
2	chr1:155267800-155276000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:155270600-155275800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:155270800-155278600	Weak transcription	Small Intestine	intestine
5	chr1:155271800-155275800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:155271800-155276000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:155271800-155276800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:155271800-155277400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:155272600-155277800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:155274200-155275800	Flanking Active TSS	Liver	Liver
11	chr1:155274200-155276400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:155274200-155276600	Enhancers	HSMM	muscle
13	chr1:155274200-155276600	Enhancers	HSMMtube	muscle
14	chr1:155274400-155276800	Enhancers	Fetal Muscle Leg	muscle
15	chr1:155274600-155275800	Enhancers	A549	lung
16	chr1:155274600-155277400	Enhancers	K562	blood
17	chr1:155274800-155275800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:155274800-155276200	Enhancers	Osteobl	bone
19	chr1:155274800-155276600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:155274800-155277800	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:155275000-155276400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:155275000-155277400	Weak transcription	Fetal Intestine Small	intestine
23	chr1:155275000-155277400	Enhancers	NHDF-Ad	bronchial
24	chr1:155275000-155278000	Weak transcription	Fetal Intestine Large	intestine
25	chr1:155275200-155276000	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr1:155275200-155276200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:155275200-155276200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:155275200-155276400	Flanking Active TSS	HepG2	liver
29	chr1:155275400-155275800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:155275400-155276200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:155275400-155276400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:155275400-155276400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:155275400-155276400	Enhancers	HMEC	breast
34	chr1:155275400-155276400	Enhancers	NHEK	skin
35	chr1:155275400-155276600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr1:155275400-155276800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:155275600-155275800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:155275600-155276000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:155275600-155276000	Enhancers	Placenta Amnion	Placenta Amnion
40	chr1:155275600-155276200	Enhancers	Colonic Mucosa	Colon
41	chr1:155275600-155277400	Weak transcription	Thymus	Thymus

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