Variant report

Variant	rs12042020
Chromosome Location	chr1:155228046-155228047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155226986..155228712-chr1:155289329..155291450,2	K562	blood:
2	chr1:155219650..155221408-chr1:155226788..155228556,2	K562	blood:
3	chr1:155218456..155235751-chr1:155288837..155299195,44	MCF-7	breast:
4	chr1:154946748..154948296-chr1:155227059..155229711,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160691	Chromatin interaction
ENSG00000160753	Chromatin interaction
ENSG00000264349	Chromatin interaction
ENSG00000160752	Chromatin interaction
ENSG00000173207	Chromatin interaction
ENSG00000225855	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10128085	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1045253	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1046188	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1052176	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1052177	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1076556	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1078699	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10796940	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10908459	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11264343	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11264345	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11264346	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11264347	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11264348	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264349	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264351	0.86[ASN][1000 genomes]
rs11264352	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264353	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264354	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264355	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264359	0.82[AFR][1000 genomes]
rs1142287	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11577338	0.94[ASN][1000 genomes]
rs12034326	0.83[ASN][1000 genomes]
rs12044063	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12049375	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12067675	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12407919	0.81[ASN][1000 genomes]
rs12563994	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12723761	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12724449	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12732972	0.84[ASN][1000 genomes]
rs12748155	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12749306	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1546818	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1800438	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1800442	0.86[AMR][1000 genomes]
rs1807042	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2009578	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2071053	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2072647	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2075566	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075569	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2236863	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236864	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242576	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2242577	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2361536	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2361543	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3020781	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34906309	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3754485	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3762272	0.84[ASN][1000 genomes]
rs3768566	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3814318	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3814319	0.89[ASN][1000 genomes]
rs4043	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4620533	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56310840	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs59062514	0.83[ASN][1000 genomes]
rs59352002	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6672284	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs734073	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs734074	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs741756	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7520184	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524950	0.82[AMR][1000 genomes]
rs7534795	0.82[AFR][1000 genomes]
rs7543234	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7549276	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7554780	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs762488	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8177968	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8847	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs932972	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9628662	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9729564	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer 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	434 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	nsv1008748	chr1:155189148-155230610	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
11	nsv1011773	chr1:155189148-155234821	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
12	esv1832331	chr1:155213136-155271366	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
13	esv1826485	chr1:155214478-155264270	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
14	esv1824971	chr1:155215985-155260869	Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
15	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
16	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
17	esv1832799	chr1:155226846-155261543	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
18	esv17013	chr1:155227059-155262674	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12042020	GBA	cis	Esophagus Mucosa	GTEx
rs12042020	THBS3	cis	Whole Blood	GTEx
rs12042020	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs12042020	GBAP1	cis	Thyroid	GTEx
rs12042020	GBAP1	cis	Artery Tibial	GTEx
rs12042020	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155225600-155228400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:155225800-155228400	Weak transcription	GM12878-XiMat	blood
3	chr1:155225800-155229600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:155225800-155230000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr1:155225800-155230200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:155225800-155230600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:155225800-155231400	Weak transcription	Aorta	Aorta
8	chr1:155226000-155228400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:155226000-155228800	Strong transcription	Brain Substantia Nigra	brain
10	chr1:155226000-155228800	Strong transcription	Thymus	Thymus
11	chr1:155226000-155229400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:155226000-155230000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:155226000-155230000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:155226000-155230000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:155226000-155230000	Strong transcription	Fetal Thymus	thymus
16	chr1:155226000-155230000	Weak transcription	K562	blood
17	chr1:155226000-155230200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:155226000-155230200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:155226000-155230200	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:155226000-155230200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:155226000-155230200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr1:155226000-155230600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr1:155226000-155230600	Weak transcription	Fetal Kidney	kidney
24	chr1:155226000-155230800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:155226000-155231000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:155226000-155231000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:155226000-155231000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:155226000-155231000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:155226000-155231200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:155226000-155231200	Weak transcription	Right Atrium	heart
31	chr1:155226200-155228400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:155226200-155228800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:155226200-155228800	Strong transcription	Brain Angular Gyrus	brain
34	chr1:155226200-155229400	Strong transcription	Brain Germinal Matrix	brain
35	chr1:155226200-155229400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:155226200-155230200	Strong transcription	Brain Anterior Caudate	brain
37	chr1:155226200-155230200	Weak transcription	Stomach Mucosa	stomach
38	chr1:155226200-155230200	Weak transcription	HMEC	breast
39	chr1:155226200-155230400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:155226200-155230400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:155226200-155230400	Strong transcription	Fetal Intestine Small	intestine
42	chr1:155226200-155230400	Strong transcription	NHLF	lung
43	chr1:155226200-155230600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:155226200-155230600	Weak transcription	NH-A	brain
45	chr1:155226200-155230800	Weak transcription	Psoas Muscle	Psoas
46	chr1:155226200-155230800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:155226200-155230800	Weak transcription	HUVEC	blood vessel
48	chr1:155226200-155231000	Strong transcription	Fetal Stomach	stomach
49	chr1:155226400-155228800	Strong transcription	HSMMtube	muscle
50	chr1:155226400-155229200	Strong transcription	Brain Hippocampus Middle	brain

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