Variant report

Variant	rs9729564
Chromosome Location	chr1:155229222-155229223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:155228937-155229446	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155229082..155234937-chr1:155291248..155296864,8	K562	blood:
2	chr1:155228693..155233633-chr1:155276892..155283389,6	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
FAM189B	TF binding region
SCAMP3	TF binding region
ENSG00000160753	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000225855	Chromatin interaction
ENSG00000160752	Chromatin interaction
ENSG00000264349	Chromatin interaction
ENSG00000173207	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10128085	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1045253	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1046188	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1052176	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1052177	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1076556	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1078699	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10796940	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10908459	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11264343	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11264345	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11264346	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264347	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11264348	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264349	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264351	0.88[ASN][1000 genomes]
rs11264352	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264353	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264354	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264355	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11264357	0.81[AMR][1000 genomes]
rs1142287	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11577338	0.95[ASN][1000 genomes]
rs12034326	0.85[ASN][1000 genomes]
rs12042020	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044063	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12049375	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12067675	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12407919	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12563994	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12723761	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12724449	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12732972	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12748155	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12749306	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1546818	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1800438	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1800442	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1807042	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2009578	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2071053	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2072647	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2075566	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2075569	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2236863	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236864	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2242576	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242577	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2361536	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2361543	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3020781	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34906309	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3754485	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3762272	0.85[ASN][1000 genomes]
rs3768566	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3814318	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3814319	0.91[ASN][1000 genomes]
rs4043	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4620533	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56310840	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs56750937	0.80[ASN][1000 genomes]
rs59062514	0.85[ASN][1000 genomes]
rs59352002	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6672284	0.84[AMR][1000 genomes]
rs734073	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs734074	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs741756	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7520184	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7524950	0.83[AMR][1000 genomes]
rs7543234	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7549276	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7554780	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762488	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8177968	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8847	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs932972	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9628662	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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
19	esv1797617	chr1:155228592-155264270	Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
20	esv1829849	chr1:155228592-155264270	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers 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	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9729564	THBS3	cis	Whole Blood	GTEx
rs9729564	GBAP1	cis	Artery Tibial	GTEx
rs9729564	GBAP1	cis	Thyroid	GTEx
rs9729564	GBA	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155225800-155229600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:155225800-155230000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:155225800-155230200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:155225800-155230600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:155225800-155231400	Weak transcription	Aorta	Aorta
6	chr1:155226000-155229400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:155226000-155230000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:155226000-155230000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:155226000-155230000	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:155226000-155230000	Strong transcription	Fetal Thymus	thymus
11	chr1:155226000-155230000	Weak transcription	K562	blood
12	chr1:155226000-155230200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:155226000-155230200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:155226000-155230200	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:155226000-155230200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:155226000-155230200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:155226000-155230600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:155226000-155230600	Weak transcription	Fetal Kidney	kidney
19	chr1:155226000-155230800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:155226000-155231000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:155226000-155231000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:155226000-155231000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:155226000-155231000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr1:155226000-155231200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:155226000-155231200	Weak transcription	Right Atrium	heart
26	chr1:155226200-155229400	Strong transcription	Brain Germinal Matrix	brain
27	chr1:155226200-155229400	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:155226200-155230200	Strong transcription	Brain Anterior Caudate	brain
29	chr1:155226200-155230200	Weak transcription	Stomach Mucosa	stomach
30	chr1:155226200-155230200	Weak transcription	HMEC	breast
31	chr1:155226200-155230400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:155226200-155230400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:155226200-155230400	Strong transcription	Fetal Intestine Small	intestine
34	chr1:155226200-155230400	Strong transcription	NHLF	lung
35	chr1:155226200-155230600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:155226200-155230600	Weak transcription	NH-A	brain
37	chr1:155226200-155230800	Weak transcription	Psoas Muscle	Psoas
38	chr1:155226200-155230800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:155226200-155230800	Weak transcription	HUVEC	blood vessel
40	chr1:155226200-155231000	Strong transcription	Fetal Stomach	stomach
41	chr1:155226400-155230000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr1:155226400-155230000	Strong transcription	Pancreas	Pancrea
43	chr1:155226400-155230000	Strong transcription	Dnd41	blood
44	chr1:155226400-155230200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:155226400-155230200	Weak transcription	Colonic Mucosa	Colon
46	chr1:155226400-155230200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:155226400-155230400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:155226400-155230400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:155226400-155230600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:155226400-155230600	Strong transcription	Brain Inferior Temporal Lobe	brain

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