Variant report

Variant	rs2072647
Chromosome Location	chr1:155221837-155221838
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155221663-155222098	PFSK-1	brain:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:155218380..155222913-chr1:155290636..155299650,10	K562	blood:
2	chr1:155210200..155211789-chr1:155219850..155222070,2	K562	blood:
3	chr1:155210207..155211789-chr1:155219850..155221900,2	K562	blood:
4	chr1:155220177..155222368-chr1:155294459..155296606,2	K562	blood:
5	chr1:155220830..155222351-chr1:155293620..155295201,2	MCF-7	breast:
6	chr1:155161177..155163523-chr1:155219674..155222613,2	K562	blood:
7	chr1:155175511..155178668-chr1:155220778..155223597,3	MCF-7	breast:
8	chr1:155218380..155223571-chr1:155290636..155294325,6	K562	blood:
9	chr1:155220296..155222214-chr1:155276999..155278896,2	K562	blood:
10	chr1:155218456..155235751-chr1:155288837..155299195,44	MCF-7	breast:
11	chr1:155220090..155222745-chr1:155275911..155279698,3	K562	blood:
12	chr1:155107455..155110019-chr1:155221050..155223424,2	MCF-7	breast:
13	chr1:155213237..155217995-chr1:155221685..155226391,8	MCF-7	breast:

No data

Variant related genes	Relation type
FAM189B	TF binding region
ENSG00000160752	Chromatin interaction
ENSG00000173171	Chromatin interaction
ENSG00000177628	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000225855	Chromatin interaction
ENSG00000160753	Chromatin interaction
ENSG00000169231	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10128085	0.80[EUR][1000 genomes]
rs1045253	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1046188	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1052176	0.88[ASN][1000 genomes]
rs1052177	0.88[ASN][1000 genomes]
rs1076556	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1078699	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10796940	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10796943	0.83[CHB][hapmap]
rs10908459	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10908463	0.84[CHB][hapmap]
rs10908465	0.84[CHB][hapmap]
rs11264337	0.89[YRI][hapmap]
rs11264338	0.89[YRI][hapmap]
rs11264339	0.89[YRI][hapmap]
rs11264343	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11264345	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11264346	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11264347	0.90[EUR][1000 genomes]
rs11264348	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11264349	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11264351	0.83[ASN][1000 genomes]
rs11264352	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11264353	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11264354	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11264355	0.81[ASN][1000 genomes]
rs11264359	0.90[CHB][hapmap]
rs11264361	0.84[CHB][hapmap]
rs11264367	0.85[CHB][hapmap]
rs11264369	0.85[CHB][hapmap]
rs11264371	0.84[CHB][hapmap]
rs11264372	0.84[CHB][hapmap]
rs1142287	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11577338	0.90[ASN][1000 genomes]
rs12026638	0.90[CHB][hapmap]
rs12034326	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12041534	0.84[CHB][hapmap]
rs12042020	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12044063	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12049375	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12067675	0.82[ASN][1000 genomes]
rs12239114	0.84[CHB][hapmap]
rs12407919	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12563994	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12723761	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12724449	0.89[ASN][1000 genomes]
rs12730000	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12748155	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12749306	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1325908	0.84[CHB][hapmap]
rs1546818	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1800438	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1800442	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1807042	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2009578	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2066981	0.86[YRI][hapmap]
rs2071053	0.88[ASN][1000 genomes]
rs2075566	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2075569	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2236863	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2236864	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2242576	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2242577	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2297480	0.95[CHB][hapmap]
rs2361536	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2361543	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28373017	0.81[ASN][1000 genomes]
rs34906309	0.84[ASN][1000 genomes]
rs3754485	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3762272	0.80[ASN][1000 genomes]
rs3768566	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3814318	0.86[ASN][1000 genomes]
rs3814319	0.86[ASN][1000 genomes]
rs4043	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4072037	0.80[YRI][hapmap]
rs4421576	0.89[YRI][hapmap]
rs4460629	0.86[YRI][hapmap]
rs4620533	0.88[ASN][1000 genomes]
rs4971079	0.93[YRI][hapmap]
rs4971085	0.90[YRI][hapmap]
rs4971088	0.90[YRI][hapmap]
rs5005770	0.84[CHB][hapmap]
rs56310840	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59352002	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs734073	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs734074	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs741756	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7520184	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7543234	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7549276	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7554780	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7556304	0.89[YRI][hapmap]
rs762488	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8177968	0.85[ASN][1000 genomes]
rs8847	0.88[ASN][1000 genomes]
rs914615	0.86[YRI][hapmap]
rs932972	0.88[ASN][1000 genomes]
rs9628662	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9729564	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv947198	chr1:155206997-155226440	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases
13	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
14	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
15	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
16	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2072647	GBA	cis	Esophagus Mucosa	GTEx
rs2072647	GBAP1	cis	Thyroid	GTEx
rs2072647	GBAP1	cis	Artery Tibial	GTEx
rs2072647	RP11-263K19.4	cis	Whole Blood	GTEx
rs2072647	THBS3	cis	Whole Blood	GTEx
rs2072647	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs2072647	RIT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155215200-155224000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155217400-155223200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:155218200-155223400	Weak transcription	Gastric	stomach
4	chr1:155218200-155223600	Weak transcription	Aorta	Aorta
5	chr1:155218400-155223400	Weak transcription	Ovary	ovary
6	chr1:155218600-155223600	Weak transcription	HSMMtube	muscle
7	chr1:155219200-155223200	Weak transcription	Fetal Lung	lung
8	chr1:155219800-155222200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:155220400-155222000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:155220600-155223200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:155220600-155223200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:155220600-155223200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:155220600-155223600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:155220600-155223800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:155220600-155223800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:155220600-155224000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:155220600-155224000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:155220600-155224600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr1:155220800-155222200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:155220800-155222200	Genic enhancers	Fetal Brain Female	brain
21	chr1:155220800-155222200	Genic enhancers	Fetal Muscle Trunk	muscle
22	chr1:155220800-155224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:155221000-155222000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:155221000-155222000	Enhancers	Brain Germinal Matrix	brain
25	chr1:155221000-155223000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:155221000-155223200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:155221000-155223200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:155221000-155223200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:155221000-155223200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:155221000-155223200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:155221000-155223200	Weak transcription	Brain Anterior Caudate	brain
32	chr1:155221000-155223200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:155221000-155223200	Weak transcription	Colonic Mucosa	Colon
34	chr1:155221000-155223200	Weak transcription	HSMM	muscle
35	chr1:155221000-155223400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:155221000-155223400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr1:155221000-155223400	Weak transcription	Brain Substantia Nigra	brain
38	chr1:155221000-155223400	Weak transcription	Esophagus	oesophagus
39	chr1:155221000-155223400	Weak transcription	Spleen	Spleen
40	chr1:155221000-155223400	Weak transcription	A549	lung
41	chr1:155221000-155223600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:155221000-155223600	Weak transcription	Lung	lung
43	chr1:155221000-155223600	Weak transcription	Small Intestine	intestine
44	chr1:155221000-155223600	Weak transcription	Stomach Mucosa	stomach
45	chr1:155221000-155223800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:155221000-155223800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr1:155221000-155223800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:155221000-155224000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr1:155221000-155224200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:155221000-155224200	Weak transcription	Thymus	Thymus

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