Variant report

Variant	rs9563084
Chromosome Location	chr13:52585993-52585994
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	STAT1	chr13:52585687-52586584	GM12878	blood:	n/a	chr13:52586510-52586521
2	CTCF	chr13:52585980-52586130	HUVEC	blood vessel:	n/a	chr13:52586072-52586085
3	MAX	chr13:52585681-52586615	A549	lung:	n/a	chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
4	YY1	chr13:52585907-52586803	GM12878	blood:	n/a	chr13:52586041-52586055 chr13:52586067-52586078 chr13:52586467-52586476 chr13:52586044-52586053 chr13:52586205-52586214
5	MAX	chr13:52585193-52586618	H1-hESC	embryonic stem cell:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
6	POLR2A	chr13:52585971-52586901	HUVEC	blood vessel:	n/a	n/a
7	EP300	chr13:52585626-52586516	ECC-1	luminal epithelium:	n/a	chr13:52586341-52586357 chr13:52586044-52586053 chr13:52586043-52586052
8	GTF2F1	chr13:52585702-52586375	K562	blood:	n/a	n/a
9	JUND	chr13:52585984-52586308	HepG2	liver:	n/a	n/a
10	RUNX3	chr13:52585979-52586748	GM12878	blood:	n/a	n/a
11	CHD2	chr13:52585455-52586705	HepG2	liver:	n/a	chr13:52586473-52586483 chr13:52586468-52586478 chr13:52586352-52586362
12	TBP	chr13:52585917-52586794	K562	blood:	n/a	n/a
13	POLR2A	chr13:52585686-52586949	H1-neurons	neurons:	n/a	n/a
14	FOSL2	chr13:52585831-52586739	HepG2	liver:	n/a	chr13:52586723-52586732
15	ZMIZ1	chr13:52585861-52586768	K562	blood:	n/a	n/a
16	POLR2A	chr13:52585640-52586798	Gliobla	brain:	n/a	n/a
17	TCF7L2	chr13:52585623-52586704	Hela-S3	cervix:	n/a	n/a
18	ZEB1	chr13:52585793-52586464	GM12878	blood:	n/a	chr13:52586150-52586161 chr13:52585971-52585978 chr13:52586149-52586158
19	ZBTB7A	chr13:52585322-52586829	ECC-1	luminal epithelium:	n/a	chr13:52586537-52586548 chr13:52585632-52585639
20	NRF1	chr13:52585961-52586692	GM12878	blood:	n/a	chr13:52586467-52586476 chr13:52586232-52586246
21	POLR2A	chr13:52585282-52586896	HepG2	liver:	n/a	n/a
22	MAX	chr13:52585691-52586169	MCF-7	breast:	n/a	chr13:52586074-52586084
23	MAX	chr13:52585033-52586745	K562	blood:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
24	RAD21	chr13:52585882-52586134	HepG2	liver:	n/a	chr13:52586070-52586082
25	MAX	chr13:52585114-52586687	K562	blood:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
26	MYBL2	chr13:52585819-52586637	HepG2	liver:	n/a	n/a
27	MAX	chr13:52585788-52586710	Hela-S3	cervix:	n/a	chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
28	HCFC1	chr13:52585928-52587048	Hela-S3	cervix:	n/a	n/a
29	HMGN3	chr13:52585268-52586527	K562	blood:	n/a	n/a
30	RAD21	chr13:52585859-52586378	HepG2	liver:	n/a	chr13:52586256-52586263 chr13:52586070-52586082
31	POLR2A	chr13:52585205-52586953	HepG2	liver:	n/a	n/a
32	POLR2A	chr13:52585346-52586916	H1-hESC	embryonic stem cell:	n/a	n/a
33	TAF1	chr13:52585766-52586737	K562	blood:	n/a	n/a
34	YY1	chr13:52585681-52586058	ECC-1	luminal epithelium:	n/a	chr13:52586041-52586055 chr13:52586044-52586053
35	TBL1XR1	chr13:52585902-52586813	GM12878	blood:	n/a	n/a
36	YY1	chr13:52585717-52586879	HepG2	liver:	n/a	chr13:52586041-52586055 chr13:52586067-52586078 chr13:52586467-52586476 chr13:52586044-52586053 chr13:52586205-52586214
37	MXI1	chr13:52585254-52586927	HepG2	liver:	n/a	n/a
38	POLR2A	chr13:52585839-52586963	SK-N-MC	brain:	n/a	n/a
39	TBP	chr13:52585493-52586789	H1-hESC	embryonic stem cell:	n/a	n/a
40	HEY1	chr13:52585786-52586288	HepG2	liver:	n/a	n/a
41	RCOR1	chr13:52585864-52586789	HepG2	liver:	n/a	n/a
42	POLR2A	chr13:52585639-52586849	H1-neurons	neurons:	n/a	n/a
43	TCF7L2	chr13:52585440-52586647	HCT-116	colon:	n/a	n/a
44	POLR2A	chr13:52585889-52586751	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr13:52585956-52586793	HEK293	kidney:	n/a	n/a
46	ZBTB7A	chr13:52585367-52586863	ECC-1	luminal epithelium:	n/a	chr13:52586537-52586548 chr13:52585632-52585639
47	PBX3	chr13:52585788-52586698	SK-N-SH	brain:	n/a	chr13:52586292-52586301
48	MAX	chr13:52585307-52586999	NB4	blood:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
49	MYC	chr13:52585302-52586719	K562	blood:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
50	EP300	chr13:52585859-52586694	HepG2	liver:	n/a	chr13:52586341-52586357 chr13:52586511-52586525 chr13:52586044-52586053 chr13:52586043-52586052

No.	Distal block	Cell Line	Cell type
1	chr1:45096767..45097715-chr13:52585858..52586559,2	NB4	blood:
2	chr13:52584477..52586900-chr13:52700506..52703372,3	K562	blood:
3	chr13:52025774..52028487-chr13:52584807..52587141,2	K562	blood:
4	chr13:52584551..52590049-chr13:52591418..52597330,6	K562	blood:
5	chr13:52585087..52587899-chr13:52598320..52601537,3	MCF-7	breast:
6	chr13:52584543..52591722-chr13:52593134..52598355,11	K562	blood:
7	chr13:52584477..52586943-chr13:52701489..52703372,3	K562	blood:
8	chr13:52158220..52159886-chr13:52585603..52588411,2	K562	blood:

Variant related genes	Relation type
ALG11	TF binding region
ATP7B	TF binding region
ENSG00000102786	Chromatin interaction
ENSG00000187147	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000253797	Chromatin interaction
ENSG00000253710	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000197168	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11616964	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11620583	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12584961	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1801243	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1801244	0.82[AMR][1000 genomes]
rs1886542	0.86[ASN][1000 genomes]
rs1886547	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1924611	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1951922	0.88[AMR][1000 genomes]
rs1998696	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2004866	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2181891	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2274202	0.85[ASN][1000 genomes]
rs2296348	0.86[ASN][1000 genomes]
rs2296349	0.86[ASN][1000 genomes]
rs2296350	0.86[ASN][1000 genomes]
rs2408544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2408549	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2408550	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2408551	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2408609	0.85[ASN][1000 genomes]
rs2408611	0.86[ASN][1000 genomes]
rs28393037	0.85[ASN][1000 genomes]
rs2897976	0.85[ASN][1000 genomes]
rs2897977	0.86[ASN][1000 genomes]
rs3368	0.86[ASN][1000 genomes]
rs35895576	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742288	0.82[AMR][1000 genomes]
rs3825527	0.82[AMR][1000 genomes]
rs3825528	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4297592	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55772266	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61958812	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6650383	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs723102	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs723103	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7327634	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7337430	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs750290	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs755363	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7993492	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7994928	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7995946	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7999812	0.82[AMR][1000 genomes]
rs9316563	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526819	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526821	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526832	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526837	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9526842	0.84[ASN][1000 genomes]
rs9535812	0.88[AMR][1000 genomes]
rs9535817	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9535819	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535822	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535823	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535826	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535828	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535829	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535830	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535832	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535833	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535836	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535849	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535851	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535858	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535860	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535862	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535866	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535872	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535878	0.85[ASN][1000 genomes]
rs9535879	0.86[ASN][1000 genomes]
rs9535880	0.86[ASN][1000 genomes]
rs9535885	0.83[ASN][1000 genomes]
rs9535887	0.84[ASN][1000 genomes]
rs9563089	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9563091	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9563093	0.84[ASN][1000 genomes]
rs9568681	0.89[AMR][1000 genomes]
rs9568693	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568695	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9568708	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9568713	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv900082	chr13:52555288-52709938	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9563084	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9563084	ALG11	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52583600-52587400	Active TSS	Fetal Intestine Small	intestine
2	chr13:52584400-52587200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr13:52584400-52587400	Active TSS	Brain Anterior Caudate	brain
4	chr13:52584400-52587400	Active TSS	Right Ventricle	heart
5	chr13:52584400-52587600	Active TSS	Right Atrium	heart
6	chr13:52584400-52587800	Active TSS	Brain Angular Gyrus	brain
7	chr13:52584600-52587400	Active TSS	Stomach Smooth Muscle	stomach
8	chr13:52584600-52587800	Active TSS	Fetal Brain Female	brain
9	chr13:52584800-52586000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr13:52584800-52586000	Active TSS	Fetal Brain Male	brain
11	chr13:52584800-52587600	Active TSS	NHDF-Ad	bronchial
12	chr13:52584800-52588000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:52584800-52588000	Active TSS	K562	blood
14	chr13:52585000-52586000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:52585000-52586000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
16	chr13:52585000-52586000	Bivalent/Poised TSS	Thymus	Thymus
17	chr13:52585000-52586200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr13:52585000-52587200	Active TSS	Fetal Kidney	kidney
19	chr13:52585000-52587200	Active TSS	Rectal Smooth Muscle	rectum
20	chr13:52585000-52587400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr13:52585000-52587400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:52585000-52587400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr13:52585000-52587400	Active TSS	Ovary	ovary
24	chr13:52585000-52587400	Active TSS	Psoas Muscle	Psoas
25	chr13:52585000-52587600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr13:52585200-52586000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
27	chr13:52585200-52586000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr13:52585200-52586000	Flanking Active TSS	Colonic Mucosa	Colon
29	chr13:52585200-52586000	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
30	chr13:52585200-52586000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
31	chr13:52585200-52586200	Flanking Bivalent TSS/Enh	Dnd41	blood
32	chr13:52585200-52587000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:52585200-52587000	Active TSS	Left Ventricle	heart
34	chr13:52585200-52587000	Active TSS	Small Intestine	intestine
35	chr13:52585200-52587200	Active TSS	Brain Cingulate Gyrus	brain
36	chr13:52585200-52587200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr13:52585200-52587200	Active TSS	Fetal Heart	heart
38	chr13:52585200-52587200	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr13:52585200-52587400	Active TSS	H9 Cell Line	embryonic stem cell
40	chr13:52585200-52587400	Active TSS	Fetal Intestine Large	intestine
41	chr13:52585200-52587600	Active TSS	Stomach Mucosa	stomach
42	chr13:52585200-52587600	Active TSS	A549	lung
43	chr13:52585400-52586000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr13:52585400-52586200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr13:52585400-52586200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr13:52585400-52586800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr13:52585400-52587000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr13:52585400-52587000	Active TSS	Esophagus	oesophagus
49	chr13:52585400-52587000	Active TSS	Gastric	stomach
50	chr13:52585400-52587000	Active TSS	Lung	lung

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