Variant report

Variant	rs56675301
Chromosome Location	chr1:155364327-155364328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10752611	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10796943	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10796944	0.85[AMR][1000 genomes]
rs10796945	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10796946	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10908465	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10908466	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10908467	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10908469	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10908470	0.84[AMR][1000 genomes]
rs10908471	0.82[AMR][1000 genomes]
rs10908472	0.82[AMR][1000 genomes]
rs11264362	0.80[ASN][1000 genomes]
rs11264363	0.82[ASN][1000 genomes]
rs11264366	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11264367	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11264369	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264370	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264371	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264372	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264374	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11264375	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11264380	0.83[EUR][1000 genomes]
rs11264381	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11264383	0.82[AMR][1000 genomes]
rs12021631	0.83[ASN][1000 genomes]
rs12024696	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12025532	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12026638	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12028416	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12037824	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12041534	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12046473	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12049455	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12067371	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12079134	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12081067	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12131079	0.83[ASN][1000 genomes]
rs12239100	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12239114	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12746592	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1325908	0.81[ASN][1000 genomes]
rs2025669	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4492610	0.83[AFR][1000 genomes]
rs5005770	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6670014	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs66923802	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71517782	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7411786	0.83[EUR][1000 genomes]
rs7416976	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7556102	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking 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
5	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
6	esv1795478	chr1:155334933-155510824	Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1803551	chr1:155334933-155522572	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv872467	chr1:155345641-155377171	Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56675301	GBA	cis	Esophagus Mucosa	GTEx
rs56675301	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs56675301	GBAP1	cis	Artery Tibial	GTEx
rs56675301	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155306200-155375400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155312400-155407400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:155340800-155364800	Weak transcription	Small Intestine	intestine
4	chr1:155345600-155403000	Weak transcription	Esophagus	oesophagus
5	chr1:155347400-155407400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:155347600-155368400	Weak transcription	Colonic Mucosa	Colon
7	chr1:155347600-155376000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:155348200-155373800	Weak transcription	Spleen	Spleen
9	chr1:155348200-155380800	Weak transcription	HMEC	breast
10	chr1:155348200-155386000	Weak transcription	NHEK	skin
11	chr1:155349400-155407600	Weak transcription	Aorta	Aorta
12	chr1:155349800-155364600	Weak transcription	HepG2	liver
13	chr1:155349800-155390800	Weak transcription	Brain Anterior Caudate	brain
14	chr1:155349800-155403000	Weak transcription	NHLF	lung
15	chr1:155350000-155399200	Weak transcription	Brain Angular Gyrus	brain
16	chr1:155350000-155402400	Weak transcription	Brain Substantia Nigra	brain
17	chr1:155350200-155399200	Weak transcription	NH-A	brain
18	chr1:155354400-155366200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr1:155355000-155367000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:155355200-155365800	Strong transcription	Liver	Liver
21	chr1:155355600-155369000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:155356400-155366000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:155356800-155366600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:155357000-155365800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr1:155357200-155366000	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr1:155357200-155400600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:155358200-155398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:155358400-155364800	Weak transcription	Ovary	ovary
29	chr1:155358600-155397000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:155358800-155364400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:155358800-155365200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:155358800-155368600	Weak transcription	Gastric	stomach
33	chr1:155359400-155407200	Weak transcription	Pancreas	Pancrea
34	chr1:155359600-155375400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:155360800-155365800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:155360800-155369200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:155361000-155365200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:155361000-155365400	Strong transcription	Adipose Nuclei	Adipose
39	chr1:155361000-155366000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:155361000-155369600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr1:155361200-155364400	Strong transcription	HSMM	muscle
42	chr1:155361200-155364400	Strong transcription	K562	blood
43	chr1:155361200-155365400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:155361200-155365400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr1:155361200-155365600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:155361200-155366000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:155361200-155370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr1:155361400-155365200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:155361400-155365400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:155361400-155365600	Strong transcription	Fetal Muscle Trunk	muscle

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