Variant report

Variant	rs3892792
Chromosome Location	chr1:155558665-155558666
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:155532514..155534121-chr1:155558467..155559967,2	K562	blood:

Variant related genes	Relation type
ENSG00000116539	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10752611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes]
rs10796943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap]
rs10796945	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs10908465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10908469	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10908470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[EUR][1000 genomes]
rs10908471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10908472	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10908479	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs10908481	0.84[CEU][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs11264369	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264371	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs11264372	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11264375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs11264380	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11264381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11264383	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11264386	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11264387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11264393	0.95[EUR][1000 genomes]
rs11264397	0.92[EUR][1000 genomes]
rs11264398	0.92[EUR][1000 genomes]
rs12022088	0.92[EUR][1000 genomes]
rs12026638	0.92[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs12030596	0.93[EUR][1000 genomes]
rs12035524	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.85[MEX][hapmap];0.83[MKK][hapmap]
rs12039893	0.92[EUR][1000 genomes]
rs12040100	0.92[EUR][1000 genomes]
rs12041534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs12047626	0.87[EUR][1000 genomes]
rs12047756	0.81[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes]
rs12079134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12091730	0.81[EUR][1000 genomes]
rs12093350	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12143948	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12724079	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs12740629	0.87[EUR][1000 genomes]
rs12744132	0.80[CEU][hapmap];0.92[JPT][hapmap]
rs12746592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[EUR][1000 genomes]
rs12758945	0.86[EUR][1000 genomes]
rs1325908	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs1360554	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs1556488	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]
rs1886905	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs2048431	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs2175391	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs2666826	0.91[JPT][hapmap]
rs34124416	0.94[EUR][1000 genomes]
rs34620961	0.88[EUR][1000 genomes]
rs348186	0.87[EUR][1000 genomes]
rs348196	0.80[CEU][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap]
rs35615695	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs3738590	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs3851912	0.94[EUR][1000 genomes]
rs4550031	0.82[EUR][1000 genomes]
rs475550	0.96[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs4971095	0.92[EUR][1000 genomes]
rs6427278	0.95[EUR][1000 genomes]
rs6427286	0.92[JPT][hapmap]
rs644853	0.92[JPT][hapmap]
rs6672128	0.89[EUR][1000 genomes]
rs6684889	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs6688636	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs6696888	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs670876	0.80[CEU][hapmap]
rs678157	0.80[CEU][hapmap];0.93[JPT][hapmap]
rs7411786	0.89[EUR][1000 genomes]
rs7521594	0.89[EUR][1000 genomes]
rs7541060	0.92[JPT][hapmap]
rs7556102	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs821551	0.84[CHB][hapmap];0.88[CHD][hapmap];1.00[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	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
4	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
5	nsv1002390	chr1:155553423-155706930	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv428246	chr1:155558197-155785831	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3892792	GBAP1	cis	Artery Tibial	GTEx
rs3892792	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs3892792	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs3892792	GBA	cis	Esophagus Mucosa	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155534600-155560400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:155534600-155565800	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:155534800-155561800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr1:155534800-155565600	Weak transcription	Brain Angular Gyrus	brain
5	chr1:155534800-155568400	Weak transcription	Thymus	Thymus
6	chr1:155535000-155560000	Weak transcription	Right Ventricle	heart
7	chr1:155535000-155570400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:155535400-155564000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:155538200-155560000	Weak transcription	Lung	lung
10	chr1:155540400-155565800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:155541400-155560400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:155541400-155561800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:155541400-155569000	Weak transcription	HSMMtube	muscle
14	chr1:155541600-155565600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:155541600-155565600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:155541600-155568400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:155541800-155560200	Weak transcription	Fetal Intestine Small	intestine
18	chr1:155542000-155565600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:155542200-155562800	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:155542400-155559800	Weak transcription	Fetal Stomach	stomach
21	chr1:155545000-155560400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:155554000-155566400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:155554200-155560400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:155557200-155568600	Weak transcription	NHEK	skin
25	chr1:155558400-155568600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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