Variant report

Variant	rs61957257
Chromosome Location	chr13:52769702-52769703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:149)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:149 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr13:52769674-52769794	Lung_OC	lung:	n/a	n/a
2	TBP	chr13:52769631-52769984	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr13:52769580-52769730	GM12872	blood:	n/a	n/a
4	CTCF	chr13:52769627-52769840	IMR90	lung:	n/a	n/a
5	CTCF	chr13:52769660-52769810	AG09319	gingival:	n/a	n/a
6	MYC	chr13:52769585-52770028	MCF-7	breast:	n/a	n/a
7	STAT5A	chr13:52769437-52769736	GM12878	blood:	n/a	n/a
8	POLR2A	chr13:52769697-52770041	H1-hESC	embryonic stem cell:	n/a	n/a
9	BHLHE40	chr13:52769225-52769853	GM12878	blood:	n/a	chr13:52769765-52769781 chr13:52769600-52769616 chr13:52769767-52769783
10	CTCF	chr13:52769700-52769850	AG04449	skin:	n/a	n/a
11	CTCF	chr13:52769640-52769790	AG10803	skin:	n/a	n/a
12	CTCF	chr13:52769648-52769876	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr13:52769620-52769770	HEEpiC	esophagus:	n/a	n/a
14	GABPA	chr13:52769407-52770163	MCF-7	breast:	n/a	n/a
15	POLR2A	chr13:52769334-52770094	PANC-1	pancreas:	n/a	n/a
16	BRCA1	chr13:52769504-52769850	H1-hESC	embryonic stem cell:	n/a	chr13:52769657-52769666
17	MAX	chr13:52769518-52770048	HUVEC	blood vessel:	n/a	chr13:52769583-52769593
18	MAX	chr13:52769523-52769984	MCF-7	breast:	n/a	chr13:52769583-52769593
19	POLR2A	chr13:52769478-52770099	HUVEC	blood vessel:	n/a	n/a
20	RCOR1	chr13:52769536-52769907	GM12878	blood:	n/a	n/a
21	CTCF	chr13:52769660-52769810	SK-N-SH_RA	brain:	n/a	n/a
22	RUNX3	chr13:52769499-52769940	GM12878	blood:	n/a	n/a
23	CTCF	chr13:52769620-52769770	GM12871	blood:	n/a	n/a
24	ZBTB33	chr13:52769469-52769897	GM12878	blood:	n/a	chr13:52769655-52769665 chr13:52769563-52769573
25	NFYB	chr13:52769638-52769978	GM12878	blood:	n/a	n/a
26	POLR2A	chr13:52769652-52770045	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr13:52769601-52769850	MCF-7	breast:	n/a	n/a
28	MXI1	chr13:52769352-52769803	GM12878	blood:	n/a	n/a
29	CTCF	chr13:52769635-52769789	ProgFib	skin:	n/a	n/a
30	CTCF	chr13:52769580-52769730	HRE	kidney:	n/a	n/a
31	MYC	chr13:52769608-52769999	MCF-7	breast:	n/a	n/a
32	POLR2A	chr13:52769517-52769965	GM12878	blood:	n/a	n/a
33	SIN3AK20	chr13:52769473-52770083	MCF-7	breast:	n/a	n/a
34	CTCF	chr13:52769665-52769801	Pancreas_OC	pancreas:	n/a	n/a
35	CTCF	chr13:52769680-52769830	HMF	breast:	n/a	n/a
36	POLR2A	chr13:52769384-52770186	MCF-7	breast:	n/a	n/a
37	SP4	chr13:52769685-52769913	H1-hESC	embryonic stem cell:	n/a	chr13:52769831-52769847
38	HA-E2F1	chr13:52769353-52769997	MCF-7	breast:	n/a	chr13:52769831-52769838 chr13:52769830-52769842 chr13:52769831-52769838 chr13:52769831-52769838
39	TBP	chr13:52769623-52769911	GM12878	blood:	n/a	n/a
40	CTCF	chr13:52769640-52769790	HVMF	connective:	n/a	n/a
41	CTCF	chr13:52769640-52769790	GM12869	blood:	n/a	n/a
42	USF2	chr13:52769667-52769862	H1-hESC	embryonic stem cell:	n/a	chr13:52769765-52769781 chr13:52769767-52769783
43	CTCF	chr13:52769660-52769810	AG10803	skin:	n/a	n/a
44	MAX	chr13:52769493-52770111	H1-hESC	embryonic stem cell:	n/a	chr13:52769583-52769593
45	GABPA	chr13:52769495-52769948	MCF-7	breast:	n/a	n/a
46	CTCF	chr13:52769600-52769750	GM12867	blood:	n/a	n/a
47	CTCF	chr13:52769620-52769770	HUVEC	blood vessel:	n/a	n/a
48	CTCF	chr13:52769619-52769858	Spleen_OC	spleen:	n/a	n/a
49	POLR2A	chr13:52769378-52770167	MCF-7	breast:	n/a	n/a
50	CTCF	chr13:52769617-52769838	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:52769662-52769712	MCF10A-Er-Src	breast:	n/a
2	chr13:52769662-52769712	A549	lung:	n/a
3	chr13:52769662-52769712	T-47D	breast:	n/a
4	chr13:52769662-52769712	IMR90	lung:	fetal
5	chr13:52769662-52769712	PANC-1	pancreas:	n/a
6	chr13:52769662-52769712	GM19239	blood:	n/a
7	chr13:52769662-52769712	U87	brain:	n/a
8	chr13:52769662-52769712	NHBE	bronchial:	n/a
9	chr13:52769662-52769712	NH-A	brain:	n/a
10	chr13:52769662-52769712	SKMC	muscle:	n/a
11	chr13:52769662-52769712	AG10803	skin:	n/a
12	chr13:52769662-52769712	CMK	blood:	n/a
13	chr13:52769662-52769712	HPAEpiC	pulmonary alveolar:	n/a
14	chr13:52769662-52769712	RPTEC	kidney:	n/a
15	chr13:52769662-52769712	HCPEpiC	choroid plexus:	n/a
16	chr13:52769662-52769712	HCT-116	colon:	n/a
17	chr13:52769662-52769712	HRCEpiC	kidney:	n/a
18	chr13:52769662-52769712	PFSK-1	brain:	n/a
19	chr13:52769662-52769712	SK-N-MC	brain:	n/a
20	chr13:52769662-52769712	GM12878	blood:	n/a
21	chr13:52769662-52769712	BE2_C	brain:	n/a
22	chr13:52769662-52769712	HMEC	breast:	n/a
23	chr13:52769662-52769712	HCF	heart:	n/a
24	chr13:52769662-52769712	LNCaP	prostate:	n/a
25	chr13:52769662-52769712	HNPCEpiC	eye:	n/a
26	chr13:52769662-52769712	HepG2	liver:	n/a
27	chr13:52769662-52769712	AoSMC	blood vessel:	n/a
28	chr13:52769662-52769712	Jurkat	blood:	n/a
29	chr13:52769662-52769712	MCF-7	breast:	n/a
30	chr13:52769662-52769712	Caco-2	colon:	n/a
31	chr13:52769662-52769712	NHDF-neo	bronchial:	n/a
32	chr13:52769662-52769712	SK-N-SH	brain:	n/a
33	chr13:52769662-52769712	ECC-1	luminal epithelium:	n/a
34	chr13:52769662-52769712	SK-N-SH_RA	brain:	n/a
35	chr13:52769662-52769712	PrEC	prostate:	n/a
36	chr13:52769662-52769712	AG04450	lung:	fetal
37	chr13:52769662-52769712	Hepatocyte	liver:	n/a
38	chr13:52769662-52769712	GM12892	blood:	n/a
39	chr13:52769662-52769712	AG09309	skin:	n/a
40	chr13:52769662-52769712	NT2-D1	testis:	n/a
41	chr13:52769662-52769712	HAEpiC	amniotic membrane:	n/a
42	chr13:52769662-52769712	AG09319	gingival:	n/a
43	chr13:52769662-52769712	ProgFib	skin:	n/a
44	chr13:52769662-52769712	HEEpiC	esophagus:	n/a
45	chr13:52769662-52769712	NB4	blood:	n/a
46	chr13:52769662-52769712	ovcar-3	ovarian:	n/a
47	chr13:52769662-52769712	HEK293	kidney:	embryo
48	chr13:52769662-52769712	Hela-S3	cervix:	n/a
49	chr13:52769662-52769712	BJ	skin:	n/a
50	chr13:52769662-52769712	HRE	kidney:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52377591..52379548-chr13:52768375..52770242,2	K562	blood:
2	chr13:52701771..52705558-chr13:52767896..52769871,3	MCF-7	breast:
3	chr13:52377651..52379551-chr13:52768569..52770283,3	MCF-7	breast:
4	chr13:52730788..52732496-chr13:52768343..52769860,2	MCF-7	breast:

No data

Variant related genes	Relation type
MRPS31P5	TF binding region
MRPS31P5	CpG island
ENSG00000231856	Chromatin interaction
ENSG00000102796	Chromatin interaction
ENSG00000197168	Chromatin interaction
ENSG00000136098	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4369550	0.82[EUR][1000 genomes]
rs56033750	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535895	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs61957257	CKAP2	cis	Heart Left Ventricle	GTEx
rs61957257	CKAP2	cis	Thyroid	GTEx
rs61957257	CKAP2	cis	Adipose Subcutaneous	GTEx
rs61957257	CKAP2	cis	Artery Tibial	GTEx
rs61957257	CKAP2	cis	lung	GTEx
rs61957257	CKAP2	cis	Nerve Tibial	GTEx
rs61957257	NEK3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52766400-52770000	Active TSS	Right Atrium	heart
2	chr13:52767200-52770000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr13:52767200-52770000	Active TSS	Psoas Muscle	Psoas
4	chr13:52767200-52770200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr13:52767400-52769800	Active TSS	Muscle Satellite Cultured Cells	--
6	chr13:52767400-52769800	Active TSS	NHDF-Ad	bronchial
7	chr13:52767400-52770000	Active TSS	H1 Cell Line	embryonic stem cell
8	chr13:52767400-52770000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr13:52767400-52770000	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr13:52767400-52770000	Active TSS	Brain Cingulate Gyrus	brain
11	chr13:52767400-52770000	Active TSS	Colonic Mucosa	Colon
12	chr13:52767400-52770000	Active TSS	Left Ventricle	heart
13	chr13:52767400-52770000	Active TSS	NHLF	lung
14	chr13:52767600-52769800	Active TSS	Duodenum Mucosa	Duodenum
15	chr13:52767600-52769800	Active TSS	Fetal Intestine Small	intestine
16	chr13:52767600-52769800	Active TSS	Rectal Smooth Muscle	rectum
17	chr13:52767600-52769800	Active TSS	HSMM	muscle
18	chr13:52767600-52770000	Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr13:52767600-52770000	Active TSS	Brain Angular Gyrus	brain
20	chr13:52767600-52770000	Active TSS	Colon Smooth Muscle	Colon
21	chr13:52767600-52770000	Active TSS	Fetal Kidney	kidney
22	chr13:52767600-52770000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr13:52767600-52770000	Active TSS	Thymus	Thymus
24	chr13:52767600-52770000	Active TSS	NH-A	brain
25	chr13:52767600-52770200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr13:52767800-52769800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr13:52767800-52769800	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr13:52767800-52769800	Active TSS	Esophagus	oesophagus
29	chr13:52767800-52769800	Active TSS	Gastric	stomach
30	chr13:52767800-52769800	Active TSS	Ovary	ovary
31	chr13:52767800-52769800	Active TSS	Pancreas	Pancrea
32	chr13:52767800-52770000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr13:52767800-52770000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr13:52767800-52770000	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr13:52767800-52770000	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr13:52767800-52770000	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr13:52767800-52770000	Active TSS	Fetal Intestine Large	intestine
38	chr13:52767800-52770000	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr13:52767800-52770000	Active TSS	Fetal Lung	lung
40	chr13:52767800-52770000	Active TSS	NHEK	skin
41	chr13:52767800-52770200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr13:52768000-52769800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr13:52768000-52769800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr13:52768000-52769800	Active TSS	Aorta	Aorta
45	chr13:52768000-52769800	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr13:52768000-52770000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr13:52768000-52770000	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr13:52768000-52770000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr13:52768000-52770000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr13:52768000-52770000	Active TSS	Brain Anterior Caudate	brain

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