Variant report

Variant	rs10908469
Chromosome Location	chr1:155468732-155468733
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155457376..155459656-chr1:155466339..155468887,2	MCF-7	breast:
2	chr1:155466285..155469139-chr1:155473048..155474657,2	K562	blood:
3	chr1:155447924..155449815-chr1:155468121..155471028,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YY1AP1-6	chr1:155468645-155468954	NONHSAT006740

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10752611	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10796943	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10796945	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10796946	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10908463	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10908465	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10908466	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10908467	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10908470	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs10908471	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs10908472	0.82[EUR][1000 genomes]
rs10908479	0.92[CEU][hapmap];0.92[JPT][hapmap]
rs11264359	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11264361	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11264363	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11264367	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264369	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264370	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11264371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11264372	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs11264374	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264375	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11264380	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11264381	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11264383	0.82[EUR][1000 genomes]
rs11264387	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs12025532	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12026638	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12028416	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12030596	0.83[EUR][1000 genomes]
rs12035524	0.91[JPT][hapmap]
rs12037824	0.81[AMR][1000 genomes]
rs12041534	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12046473	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12047756	0.92[JPT][hapmap]
rs12067371	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12079134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12081067	0.81[EUR][1000 genomes]
rs12143948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12239100	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12239114	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12724079	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12744132	0.92[JPT][hapmap]
rs12746592	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1325908	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1360554	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1556488	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs1886905	0.92[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap]
rs2025669	0.83[EUR][1000 genomes]
rs2048431	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2175391	0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2297480	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs2666826	0.91[JPT][hapmap]
rs348196	0.91[JPT][hapmap]
rs35615695	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3738590	0.92[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap]
rs3892792	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs475550	0.92[CEU][hapmap];0.91[JPT][hapmap]
rs5005770	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56675301	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6684889	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs6688636	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6696888	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs678157	0.92[JPT][hapmap]
rs7411786	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7416976	0.81[EUR][1000 genomes]
rs7556102	0.85[CHB][hapmap];0.92[JPT][hapmap]

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	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	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
4	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
5	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
6	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
7	esv1800974	chr1:155367680-155510824	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10908469	GBA	cis	Esophagus Mucosa	GTEx
rs10908469	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs10908469	GBAP1	cis	Artery Tibial	GTEx

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155442200-155469800	Weak transcription	Small Intestine	intestine
2	chr1:155443200-155470400	Weak transcription	Right Ventricle	heart
3	chr1:155449000-155469400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:155450000-155483000	Weak transcription	NHLF	lung
5	chr1:155452000-155488800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:155452200-155469000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:155452200-155469000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:155452200-155469000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:155452200-155469000	Weak transcription	NHEK	skin
10	chr1:155452200-155469200	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:155452200-155469400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:155452200-155469600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:155452200-155469600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:155452200-155469600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:155452200-155469600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:155452200-155469600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:155452200-155469800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:155452200-155469800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:155452200-155469800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr1:155452200-155469800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:155452200-155469800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:155452200-155469800	Weak transcription	Adipose Nuclei	Adipose
23	chr1:155452200-155469800	Weak transcription	Fetal Intestine Large	intestine
24	chr1:155452200-155469800	Weak transcription	Fetal Lung	lung
25	chr1:155452200-155469800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:155452200-155469800	Weak transcription	Right Atrium	heart
27	chr1:155452200-155469800	Weak transcription	Hela-S3	cervix
28	chr1:155452200-155470200	Weak transcription	Spleen	Spleen
29	chr1:155452200-155475000	Weak transcription	K562	blood
30	chr1:155452200-155477400	Weak transcription	Lung	lung
31	chr1:155452200-155481400	Weak transcription	Thymus	Thymus
32	chr1:155452200-155482400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:155452400-155468800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:155452400-155469000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:155452400-155469200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:155452400-155469200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:155452400-155469400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:155452400-155469600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:155452400-155469600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:155452400-155469600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:155452400-155469800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:155452400-155483000	Weak transcription	HSMM	muscle
43	chr1:155452400-155505200	Weak transcription	Placenta	Placenta
44	chr1:155452800-155469600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr1:155453400-155477200	Weak transcription	Dnd41	blood
46	chr1:155455400-155470200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:155455800-155468800	Weak transcription	Primary B cells from cord blood	blood
48	chr1:155456200-155469000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:155456200-155469400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:155456200-155469600	Weak transcription	A549	lung

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