Variant report

Variant	rs6561658
Chromosome Location	chr13:52734151-52734152
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:62)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:62 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:52733403-52734160	HL-60	blood:	n/a	n/a
2	MYBL2	chr13:52733340-52734238	HepG2	liver:	n/a	n/a
3	MAX	chr13:52733105-52734312	ECC-1	luminal epithelium:	n/a	n/a
4	ELF1	chr13:52733364-52734158	HepG2	liver:	n/a	n/a
5	E2F4	chr13:52733607-52734191	MCF10A-Er-Src	breast:	n/a	n/a
6	NFIC	chr13:52733652-52734187	HepG2	liver:	n/a	n/a
7	CBX3	chr13:52733555-52734397	HCT-116	colon:	n/a	n/a
8	MBD4	chr13:52733689-52734292	HepG2	liver:	n/a	n/a
9	MAX	chr13:52733650-52734237	H1-hESC	embryonic stem cell:	n/a	n/a
10	GTF2F1	chr13:52733735-52734163	Hela-S3	cervix:	n/a	n/a
11	EP300	chr13:52733560-52734203	HepG2	liver:	n/a	chr13:52733650-52733666
12	EP300	chr13:52733650-52734234	HepG2	liver:	n/a	chr13:52733650-52733666
13	E2F6	chr13:52733091-52734548	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr13:52732970-52734237	MCF10A-Er-Src	breast:	n/a	n/a
15	EP300	chr13:52733773-52734152	GM12878	blood:	n/a	n/a
16	KAP1	chr13:52733319-52734204	HEK293	kidney:	n/a	n/a
17	SIN3A	chr13:52732989-52734210	H1-hESC	embryonic stem cell:	n/a	n/a
18	TCF12	chr13:52733451-52734234	A549	lung:	n/a	n/a
19	TBP	chr13:52733504-52734239	HepG2	liver:	n/a	n/a
20	POLR2A	chr13:52732918-52734186	SK-N-MC	brain:	n/a	n/a
21	MXI1	chr13:52733340-52734161	HepG2	liver:	n/a	n/a
22	HA-E2F1	chr13:52733104-52734181	MCF-7	breast:	n/a	n/a
23	E2F6	chr13:52733039-52734363	K562	blood:	n/a	n/a
24	CBX3	chr13:52733509-52734229	HCT-116	colon:	n/a	n/a
25	MYBL2	chr13:52733615-52734240	HepG2	liver:	n/a	n/a
26	MAX	chr13:52733212-52734161	K562	blood:	n/a	n/a
27	MAX	chr13:52732936-52734152	SK-N-SH	brain:	n/a	n/a
28	CEBPB	chr13:52733857-52734200	HepG2	liver:	n/a	n/a
29	E2F6	chr13:52733462-52734155	K562	blood:	n/a	n/a
30	TEAD4	chr13:52733660-52734237	HepG2	liver:	n/a	n/a
31	MAX	chr13:52733210-52734296	HepG2	liver:	n/a	n/a
32	MAX	chr13:52733076-52734291	HepG2	liver:	n/a	n/a
33	E2F6	chr13:52733287-52734305	H1-hESC	embryonic stem cell:	n/a	n/a
34	HEY1	chr13:52733349-52734209	HepG2	liver:	n/a	chr13:52733571-52733586
35	ELF1	chr13:52733392-52734160	HepG2	liver:	n/a	n/a
36	E2F6	chr13:52733352-52734307	A549	lung:	n/a	n/a
37	MAX	chr13:52733300-52734178	H1-hESC	embryonic stem cell:	n/a	n/a
38	HEY1	chr13:52733431-52734156	HepG2	liver:	n/a	chr13:52733571-52733586
39	POLR2A	chr13:52732959-52734291	HepG2	liver:	n/a	n/a
40	E2F6	chr13:52733485-52734188	Hela-S3	cervix:	n/a	n/a
41	MAX	chr13:52733523-52734268	MCF-7	breast:	n/a	n/a
42	CBX3	chr13:52733579-52734234	K562	blood:	n/a	n/a
43	NFIC	chr13:52733653-52734212	HepG2	liver:	n/a	n/a
44	HDAC2	chr13:52733249-52734183	HepG2	liver:	n/a	n/a
45	MAX	chr13:52733365-52734284	HCT-116	colon:	n/a	n/a
46	MAX	chr13:52733392-52734211	A549	lung:	n/a	n/a
47	POLR2A	chr13:52733373-52734234	HepG2	liver:	n/a	n/a
48	POLR2A	chr13:52732549-52734480	HepG2	liver:	n/a	n/a
49	JUN	chr13:52733397-52734193	K562	blood:	n/a	n/a
50	SETDB1	chr13:52733760-52734200	U2OS	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:52734134-52734184	HRE	kidney:	n/a
2	chr13:52734134-52734184	H1-hESC	embryonic stem cell:	embryo
3	chr13:52734134-52734184	AG09309	skin:	n/a
4	chr13:52734134-52734184	HEEpiC	esophagus:	n/a
5	chr13:52734134-52734184	BJ	skin:	n/a
6	chr13:52734134-52734184	Hela-S3	cervix:	n/a
7	chr13:52734134-52734184	SAEC	small airway:	n/a
8	chr13:52734134-52734184	AG09319	gingival:	n/a
9	chr13:52734134-52734184	PANC-1	pancreas:	n/a
10	chr13:52734134-52734184	CMK	blood:	n/a
11	chr13:52734134-52734184	SK-N-SH	brain:	n/a
12	chr13:52734134-52734184	Caco-2	colon:	n/a
13	chr13:52734134-52734184	NB4	blood:	n/a
14	chr13:52734134-52734184	HepG2	liver:	n/a
15	chr13:52734134-52734184	IMR90	lung:	fetal
16	chr13:52734134-52734184	HCPEpiC	choroid plexus:	n/a
17	chr13:52734134-52734184	AG04450	lung:	fetal
18	chr13:52734134-52734184	HUVEC	blood vessel:	n/a
19	chr13:52734134-52734184	HCT-116	colon:	n/a
20	chr13:52734134-52734184	GM06990	blood:	n/a
21	chr13:52734134-52734184	AG10803	skin:	n/a
22	chr13:52734134-52734184	GM12891	blood:	n/a
23	chr13:52734134-52734184	K562	blood:	n/a
24	chr13:52734134-52734184	HIPEpiC	eye:	n/a
25	chr13:52734134-52734184	HMEC	breast:	n/a
26	chr13:52734134-52734184	BE2_C	brain:	n/a
27	chr13:52734134-52734184	SK-N-SH_RA	brain:	n/a
28	chr13:52734134-52734184	HEK293	kidney:	embryo
29	chr13:52734134-52734184	HRCEpiC	kidney:	n/a
30	chr13:52734134-52734184	PFSK-1	brain:	n/a
31	chr13:52734134-52734184	HAEpiC	amniotic membrane:	n/a
32	chr13:52734134-52734184	T-47D	breast:	n/a
33	chr13:52734134-52734184	AoSMC	blood vessel:	n/a
34	chr13:52734134-52734184	HCF	heart:	n/a
35	chr13:52734134-52734184	HCM	heart:	n/a
36	chr13:52734134-52734184	MCF-7	breast:	n/a
37	chr13:52734134-52734184	ovcar-3	ovarian:	n/a
38	chr13:52734134-52734184	GM12878	blood:	n/a
39	chr13:52734134-52734184	GM19239	blood:	n/a
40	chr13:52734134-52734184	LNCaP	prostate:	n/a
41	chr13:52734134-52734184	AG04449	skin:	fetal
42	chr13:52734134-52734184	NH-A	brain:	n/a
43	chr13:52734134-52734184	NHBE	bronchial:	n/a
44	chr13:52734134-52734184	NT2-D1	testis:	n/a
45	chr13:52734134-52734184	Jurkat	blood:	n/a
46	chr13:52734134-52734184	SK-N-MC	brain:	n/a
47	chr13:52734134-52734184	HNPCEpiC	eye:	n/a
48	chr13:52734134-52734184	HRPEpiC	eye:	n/a
49	chr13:52734134-52734184	PrEC	prostate:	n/a
50	chr13:52734134-52734184	U87	brain:	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: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1004576	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs1055062	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs1060631	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs1134727	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12146904	0.86[CHB][hapmap]
rs12431310	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs1571189	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1886539	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1886542	0.89[CEU][hapmap]
rs1886543	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap]
rs1886544	0.82[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2274202	0.89[CEU][hapmap]
rs2277448	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2296347	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2296348	0.89[CEU][hapmap]
rs2296349	0.89[CEU][hapmap]
rs2408552	0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2408554	0.86[CHB][hapmap]
rs2408609	0.92[CEU][hapmap]
rs2408611	0.92[CEU][hapmap]
rs2897964	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs2897965	0.84[ASN][1000 genomes]
rs2897977	0.89[CEU][hapmap]
rs3368	0.89[CEU][hapmap]
rs3742289	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs3783242	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3818422	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4497567	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs4941727	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6561656	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs66849828	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7320831	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs7321120	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs7324458	0.81[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs7332356	0.81[ASN][1000 genomes]
rs7981904	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7998770	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs9526823	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs9526825	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs9526835	0.84[ASN][1000 genomes]
rs9526841	0.87[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9526842	0.89[CEU][hapmap]
rs9526843	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9535853	0.81[ASN][1000 genomes]
rs9535867	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs9535871	0.84[ASN][1000 genomes]
rs9535873	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs9535878	0.89[CEU][hapmap]
rs9535879	0.92[CEU][hapmap]
rs9535880	0.89[CEU][hapmap]
rs9535882	0.89[CEU][hapmap]
rs9535883	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535885	0.89[CEU][hapmap]
rs9535887	0.89[CEU][hapmap]
rs9535888	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535889	0.80[AMR][1000 genomes];0.87[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
rs6561658	CKAP2	cis	Artery Tibial	GTEx
rs6561658	NEK3	cis	normal skin	skin_eQTL
rs6561658	CKAP2	cis	Nerve Tibial	GTEx
rs6561658	NEK3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52732600-52734200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr13:52732600-52734200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:52732600-52734200	Active TSS	Aorta	Aorta
4	chr13:52732800-52734200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:52732800-52734200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:52732800-52734200	Active TSS	Fetal Brain Male	brain
7	chr13:52732800-52734200	Active TSS	Fetal Muscle Trunk	muscle
8	chr13:52732800-52734200	Active TSS	Ovary	ovary
9	chr13:52732800-52734200	Active TSS	Pancreas	Pancrea
10	chr13:52732800-52734200	Active TSS	Psoas Muscle	Psoas
11	chr13:52733000-52734200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr13:52733000-52734200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr13:52733000-52734200	Active TSS	HSMMtube	muscle
14	chr13:52733000-52734400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr13:52733200-52734200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr13:52733400-52734200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr13:52733600-52734200	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr13:52733600-52734200	Active TSS	Brain Germinal Matrix	brain
19	chr13:52733600-52734200	Active TSS	Fetal Brain Female	brain
20	chr13:52733800-52734200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
21	chr13:52733800-52734200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr13:52733800-52734200	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr13:52733800-52734200	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr13:52733800-52734200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr13:52733800-52734200	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr13:52733800-52734200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr13:52733800-52734200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr13:52733800-52734200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr13:52733800-52734200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr13:52733800-52734200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr13:52733800-52734200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr13:52733800-52734200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr13:52733800-52734200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr13:52733800-52734200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr13:52733800-52734200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr13:52733800-52734200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr13:52733800-52734200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr13:52733800-52734200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr13:52733800-52734200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:52733800-52734200	Flanking Active TSS	Liver	Liver
41	chr13:52733800-52734200	Flanking Active TSS	Brain Angular Gyrus	brain
42	chr13:52733800-52734200	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr13:52733800-52734200	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr13:52733800-52734200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr13:52733800-52734200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr13:52733800-52734200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr13:52733800-52734200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr13:52733800-52734200	Flanking Active TSS	Fetal Intestine Large	intestine
49	chr13:52733800-52734200	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr13:52733800-52734200	Flanking Active TSS	Fetal Kidney	kidney

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