Variant report

Variant	rs9535889
Chromosome Location	chr13:52733634-52733635
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:206)
CpG islands
(count:122)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:206 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:52733337-52733829	GM12878	blood:	n/a	n/a
2	FOXA1	chr13:52733535-52734092	HepG2	liver:	n/a	n/a
3	POLR2A	chr13:52733403-52734160	HL-60	blood:	n/a	n/a
4	USF2	chr13:52733454-52734008	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYBL2	chr13:52733340-52734238	HepG2	liver:	n/a	n/a
6	ZBTB7A	chr13:52733213-52733877	K562	blood:	n/a	n/a
7	UBTF	chr13:52733102-52733962	K562	blood:	n/a	n/a
8	MYC	chr13:52733407-52733941	MCF-7	breast:	n/a	n/a
9	POLR2A	chr13:52733286-52734086	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr13:52733476-52733763	K562	blood:	n/a	n/a
11	MAX	chr13:52733593-52734110	MCF-7	breast:	n/a	n/a
12	RCOR1	chr13:52732775-52733821	GM12878	blood:	n/a	n/a
13	MAX	chr13:52733105-52734312	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr13:52733329-52733926	HUVEC	blood vessel:	n/a	n/a
15	MYC	chr13:52733488-52734125	MCF10A-Er-Src	breast:	n/a	n/a
16	ELF1	chr13:52733364-52734158	HepG2	liver:	n/a	n/a
17	MYC	chr13:52733585-52734090	A549	lung:	n/a	n/a
18	E2F4	chr13:52733607-52734191	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr13:52733303-52733863	GM12892	blood:	n/a	n/a
20	PAX5	chr13:52733335-52733804	GM12892	blood:	n/a	chr13:52733564-52733573 chr13:52733566-52733575
21	POLR2A	chr13:52733493-52733973	HCT-116	colon:	n/a	n/a
22	YY1	chr13:52733602-52733916	HCT-116	colon:	n/a	n/a
23	POLR2A	chr13:52732984-52734139	MCF10A-Er-Src	breast:	n/a	n/a
24	HEY1	chr13:52733545-52733823	K562	blood:	n/a	chr13:52733571-52733586
25	POLR2A	chr13:52733533-52733900	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr13:52733133-52733914	MCF-7	breast:	n/a	n/a
27	TAF1	chr13:52732922-52733927	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr13:52733313-52733898	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr13:52733254-52733856	GM15510	blood:	n/a	n/a
30	POLR2A	chr13:52733469-52734044	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAZ	chr13:52733350-52733939	K562	blood:	n/a	n/a
32	CBX3	chr13:52733555-52734397	HCT-116	colon:	n/a	n/a
33	MXI1	chr13:52732885-52734068	GM12878	blood:	n/a	n/a
34	PML	chr13:52733493-52733876	K562	blood:	n/a	n/a
35	POLR2A	chr13:52733483-52733898	K562	blood:	n/a	n/a
36	JUND	chr13:52733429-52733738	H1-hESC	embryonic stem cell:	n/a	n/a
37	MYC	chr13:52733627-52734003	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr13:52733435-52733763	A549	lung:	n/a	n/a
39	MAX	chr13:52733493-52734095	HepG2	liver:	n/a	n/a
40	MAFK	chr13:52733157-52733710	HepG2	liver:	n/a	n/a
41	POLR2A	chr13:52733347-52733880	A549	lung:	n/a	n/a
42	POLR2A	chr13:52733354-52733906	A549	lung:	n/a	n/a
43	YY1	chr13:52733524-52733797	GM12892	blood:	n/a	chr13:52733568-52733582
44	POLR2A	chr13:52733354-52733854	HUVEC	blood vessel:	n/a	n/a
45	GABPA	chr13:52733263-52733924	K562	blood:	n/a	n/a
46	POLR2A	chr13:52733386-52733964	H1-neurons	neurons:	n/a	n/a
47	EP300	chr13:52733560-52734203	HepG2	liver:	n/a	chr13:52733650-52733666
48	MXI1	chr13:52733614-52734087	H1-hESC	embryonic stem cell:	n/a	n/a
49	ELF1	chr13:52733354-52733789	GM12878	blood:	n/a	n/a
50	POLR2A	chr13:52733388-52733854	HepG2	liver:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:52733586-52733636	LNCaP	prostate:	n/a
2	chr13:52733586-52733636	GM12891	blood:	n/a
3	chr13:52733586-52733636	IMR90	lung:	fetal
4	chr13:52733586-52733636	AG04450	lung:	fetal
5	chr13:52733586-52733636	GM06990	blood:	n/a
6	chr13:52733628-52733678	BJ	skin:	n/a
7	chr13:52733586-52733636	NHDF-neo	bronchial:	n/a
8	chr13:52733628-52733678	HNPCEpiC	eye:	n/a
9	chr13:52733586-52733636	SK-N-MC	brain:	n/a
10	chr13:52733628-52733678	HUVEC	blood vessel:	n/a
11	chr13:52733586-52733636	HUVEC	blood vessel:	n/a
12	chr13:52733628-52733678	HCT-116	colon:	n/a
13	chr13:52733628-52733678	HRCEpiC	kidney:	n/a
14	chr13:52733586-52733636	HCT-116	colon:	n/a
15	chr13:52733586-52733636	PFSK-1	brain:	n/a
16	chr13:52733586-52733636	HEK293	kidney:	embryo
17	chr13:52733628-52733678	AoSMC	blood vessel:	n/a
18	chr13:52733628-52733678	HRE	kidney:	n/a
19	chr13:52733628-52733678	MCF-7	breast:	n/a
20	chr13:52733586-52733636	NB4	blood:	n/a
21	chr13:52733628-52733678	GM19239	blood:	n/a
22	chr13:52733586-52733636	AG10803	skin:	n/a
23	chr13:52733628-52733678	AG09319	gingival:	n/a
24	chr13:52733586-52733636	MCF10A-Er-Src	breast:	n/a
25	chr13:52733628-52733678	NH-A	brain:	n/a
26	chr13:52733586-52733636	NT2-D1	testis:	n/a
27	chr13:52733628-52733678	SK-N-SH	brain:	n/a
28	chr13:52733628-52733678	HMEC	breast:	n/a
29	chr13:52733628-52733678	HEK293	kidney:	embryo
30	chr13:52733586-52733636	T-47D	breast:	n/a
31	chr13:52733586-52733636	AG09319	gingival:	n/a
32	chr13:52733628-52733678	Jurkat	blood:	n/a
33	chr13:52733586-52733636	HMEC	breast:	n/a
34	chr13:52733628-52733678	NHBE	bronchial:	n/a
35	chr13:52733586-52733636	ECC-1	luminal epithelium:	n/a
36	chr13:52733586-52733636	PANC-1	pancreas:	n/a
37	chr13:52733586-52733636	BE2_C	brain:	n/a
38	chr13:52733586-52733636	AG09309	skin:	n/a
39	chr13:52733628-52733678	HCM	heart:	n/a
40	chr13:52733586-52733636	GM19239	blood:	n/a
41	chr13:52733586-52733636	Hepatocyte	liver:	n/a
42	chr13:52733628-52733678	HepG2	liver:	n/a
43	chr13:52733628-52733678	CMK	blood:	n/a
44	chr13:52733586-52733636	HAEpiC	amniotic membrane:	n/a
45	chr13:52733628-52733678	SKMC	muscle:	n/a
46	chr13:52733586-52733636	AoSMC	blood vessel:	n/a
47	chr13:52733586-52733636	SAEC	small airway:	n/a
48	chr13:52733586-52733636	HepG2	liver:	n/a
49	chr13:52733628-52733678	AG04449	skin:	fetal
50	chr13:52733628-52733678	HEEpiC	esophagus:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52729535..52732308-chr13:52732328..52734703,4	K562	blood:

No data

Variant related genes	Relation type
NEK3	TF binding region
NEK3	CpG island
ENSG00000136098	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1004576	0.92[ASN][1000 genomes]
rs1055062	0.84[ASN][1000 genomes]
rs1060631	0.84[ASN][1000 genomes]
rs1134727	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12146904	0.92[ASN][1000 genomes]
rs12431310	0.92[ASN][1000 genomes]
rs12560598	0.83[ASN][1000 genomes]
rs1571189	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1886539	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1886543	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1886544	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1886545	0.84[ASN][1000 genomes]
rs1886546	0.84[ASN][1000 genomes]
rs2005182	0.90[ASN][1000 genomes]
rs2277448	0.81[ASN][1000 genomes]
rs2296347	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2408546	0.87[ASN][1000 genomes]
rs2408547	0.88[ASN][1000 genomes]
rs2408548	0.88[ASN][1000 genomes]
rs2408552	0.85[ASN][1000 genomes]
rs2408554	0.91[ASN][1000 genomes]
rs2897964	0.84[ASN][1000 genomes]
rs2897965	0.86[ASN][1000 genomes]
rs3742289	0.84[ASN][1000 genomes]
rs3742291	0.84[ASN][1000 genomes]
rs3783242	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3818422	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4261421	0.87[ASN][1000 genomes]
rs4264295	0.88[ASN][1000 genomes]
rs4941727	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4943060	0.82[ASN][1000 genomes]
rs61958804	0.84[ASN][1000 genomes]
rs61958805	0.81[ASN][1000 genomes]
rs6561656	0.81[ASN][1000 genomes]
rs6561658	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6650384	0.88[ASN][1000 genomes]
rs6650385	0.88[ASN][1000 genomes]
rs66849828	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7318287	0.88[ASN][1000 genomes]
rs7319784	0.81[ASN][1000 genomes]
rs7320252	0.88[ASN][1000 genomes]
rs7320429	0.88[ASN][1000 genomes]
rs7320831	0.81[ASN][1000 genomes]
rs7321120	0.81[ASN][1000 genomes]
rs7321310	0.81[ASN][1000 genomes]
rs7324458	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7332356	0.84[ASN][1000 genomes]
rs7338131	0.88[ASN][1000 genomes]
rs7998770	0.91[ASN][1000 genomes]
rs9526823	0.84[ASN][1000 genomes]
rs9526825	0.85[ASN][1000 genomes]
rs9526826	0.88[ASN][1000 genomes]
rs9526834	0.90[ASN][1000 genomes]
rs9526835	0.86[ASN][1000 genomes]
rs9526836	0.92[ASN][1000 genomes]
rs9526841	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526843	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535845	0.88[ASN][1000 genomes]
rs9535853	0.84[ASN][1000 genomes]
rs9535867	0.90[ASN][1000 genomes]
rs9535871	0.87[ASN][1000 genomes]
rs9535873	0.92[ASN][1000 genomes]
rs9535883	0.84[ASN][1000 genomes]
rs9535888	0.94[ASN][1000 genomes]
rs9568692	0.88[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	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
3	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
4	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
5	nsv1037567	chr13:52643647-52802799	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer 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	esv3429935	chr13:52694751-52735744	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9535889	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9535889	NEK3	cis	Muscle Skeletal	GTEx
rs9535889	CKAP2	cis	Nerve Tibial	GTEx
rs9535889	CKAP2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52732400-52733800	Active TSS	Stomach Mucosa	stomach
2	chr13:52732400-52734000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr13:52732600-52733800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr13:52732600-52733800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:52732600-52733800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:52732600-52733800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr13:52732600-52733800	Active TSS	Fetal Stomach	stomach
8	chr13:52732600-52733800	Active TSS	Rectal Smooth Muscle	rectum
9	chr13:52732600-52733800	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr13:52732600-52734000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr13:52732600-52734000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr13:52732600-52734000	Active TSS	A549	lung
13	chr13:52732600-52734000	Active TSS	NHLF	lung
14	chr13:52732600-52734200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:52732600-52734200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:52732600-52734200	Active TSS	Aorta	Aorta
17	chr13:52732800-52733800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:52732800-52733800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr13:52732800-52733800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr13:52732800-52733800	Active TSS	Brain Anterior Caudate	brain
21	chr13:52732800-52733800	Active TSS	Brain Substantia Nigra	brain
22	chr13:52732800-52733800	Active TSS	Fetal Kidney	kidney
23	chr13:52732800-52733800	Active TSS	Placenta	Placenta
24	chr13:52732800-52733800	Active TSS	Thymus	Thymus
25	chr13:52732800-52733800	Active TSS	K562	blood
26	chr13:52732800-52734000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr13:52732800-52734000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:52732800-52734000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr13:52732800-52734000	Active TSS	Left Ventricle	heart
30	chr13:52732800-52734000	Active TSS	Right Atrium	heart
31	chr13:52732800-52734000	Active TSS	Right Ventricle	heart
32	chr13:52732800-52734200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr13:52732800-52734200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr13:52732800-52734200	Active TSS	Fetal Brain Male	brain
35	chr13:52732800-52734200	Active TSS	Fetal Muscle Trunk	muscle
36	chr13:52732800-52734200	Active TSS	Ovary	ovary
37	chr13:52732800-52734200	Active TSS	Pancreas	Pancrea
38	chr13:52732800-52734200	Active TSS	Psoas Muscle	Psoas
39	chr13:52733000-52733800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr13:52733000-52733800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:52733000-52733800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr13:52733000-52733800	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr13:52733000-52733800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr13:52733000-52733800	Active TSS	Primary monocytes fromperipheralblood	blood
45	chr13:52733000-52733800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr13:52733000-52733800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr13:52733000-52733800	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr13:52733000-52733800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr13:52733000-52733800	Active TSS	Muscle Satellite Cultured Cells	--
50	chr13:52733000-52733800	Active TSS	Cortex derived primary cultured neurospheres	brain

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