Variant report

Variant	rs1556488
Chromosome Location	chr1:155540660-155540661
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10752611	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10796943	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10796945	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10796946	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10796947	0.95[ASN][1000 genomes]
rs10908465	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs10908466	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908467	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10908469	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes]
rs10908470	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908471	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908472	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908479	0.96[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs10908481	0.84[CEU][hapmap];0.81[JPT][hapmap];0.85[TSI][hapmap]
rs11264369	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11264371	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.88[ASN][1000 genomes]
rs11264372	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs11264374	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264375	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264380	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264381	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11264383	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264386	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264387	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264393	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11264397	0.90[EUR][1000 genomes]
rs11264398	0.91[EUR][1000 genomes]
rs11582072	0.95[ASN][1000 genomes]
rs12022088	0.90[EUR][1000 genomes]
rs12026638	0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12028416	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12030596	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035524	0.80[CEU][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs12037824	0.86[ASN][1000 genomes]
rs12039893	0.90[EUR][1000 genomes]
rs12040100	0.91[EUR][1000 genomes]
rs12041534	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12046473	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12047626	0.86[EUR][1000 genomes]
rs12047756	0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs12048286	0.84[AMR][1000 genomes]
rs12067371	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12079134	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12091730	0.85[AMR][1000 genomes]
rs12093350	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12143948	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs12239100	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12724079	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs12740629	0.86[EUR][1000 genomes]
rs12744132	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs12746592	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758945	0.84[EUR][1000 genomes]
rs1325908	0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1360554	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs1886905	0.96[CEU][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs2048431	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs2175391	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs34124416	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34620961	0.86[EUR][1000 genomes]
rs348186	0.85[EUR][1000 genomes]
rs348196	0.80[CEU][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap]
rs35615695	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.97[ASN][1000 genomes]
rs3738590	0.96[CEU][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs3851912	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3892792	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs475550	0.96[CEU][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs4971095	0.91[EUR][1000 genomes]
rs5005770	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs6427278	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6427286	0.81[JPT][hapmap]
rs644853	0.90[JPT][hapmap]
rs6672128	0.87[EUR][1000 genomes]
rs6684889	0.84[CHB][hapmap];0.89[ASN][1000 genomes]
rs6688636	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.95[ASN][1000 genomes]
rs6696888	0.95[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.99[ASN][1000 genomes]
rs670876	0.81[CEU][hapmap]
rs678157	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs7411786	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7521594	0.87[EUR][1000 genomes]
rs7541060	0.81[JPT][hapmap]
rs7556102	0.90[JPT][hapmap]
rs821551	0.83[CHD][hapmap];0.90[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1556488	GBA	cis	Esophagus Mucosa	GTEx
rs1556488	GBAP1	cis	Artery Tibial	GTEx
rs1556488	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs1556488	FDPS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 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	chr1:155534200-155542800	Weak transcription	Esophagus	oesophagus
3	chr1:155534200-155543000	Weak transcription	Brain Germinal Matrix	brain
4	chr1:155534200-155547600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:155534400-155544200	Weak transcription	Fetal Brain Female	brain
6	chr1:155534600-155542000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:155534600-155542000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:155534600-155542000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:155534600-155542200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:155534600-155542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:155534600-155542400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:155534600-155542400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:155534600-155543000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:155534600-155543000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:155534600-155560400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:155534600-155565800	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:155534800-155540800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:155534800-155541000	Weak transcription	HSMMtube	muscle
19	chr1:155534800-155542200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:155534800-155542600	Weak transcription	NHLF	lung
21	chr1:155534800-155543000	Weak transcription	HepG2	liver
22	chr1:155534800-155543200	Weak transcription	Pancreas	Pancrea
23	chr1:155534800-155544800	Weak transcription	Brain Anterior Caudate	brain
24	chr1:155534800-155558200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:155534800-155561800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:155534800-155565600	Weak transcription	Brain Angular Gyrus	brain
27	chr1:155534800-155568400	Weak transcription	Thymus	Thymus
28	chr1:155535000-155541000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr1:155535000-155541800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:155535000-155543200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:155535000-155543600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:155535000-155560000	Weak transcription	Right Ventricle	heart
33	chr1:155535000-155570400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:155535200-155542000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:155535200-155542400	Weak transcription	Small Intestine	intestine
36	chr1:155535200-155542800	Weak transcription	Placenta	Placenta
37	chr1:155535400-155542800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:155535400-155543800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:155535400-155564000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:155535600-155542000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:155535800-155541600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:155536000-155542600	Weak transcription	NHDF-Ad	bronchial
43	chr1:155536000-155544000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:155536000-155545200	Weak transcription	HMEC	breast
45	chr1:155536200-155542800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:155536200-155543200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:155536200-155544400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:155537000-155543800	Weak transcription	Primary B cells from cord blood	blood
49	chr1:155537000-155544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:155537000-155544800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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