Variant report

Variant	rs61958788
Chromosome Location	chr13:52585313-52585314
allele	C/T
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	CTCF	chr13:52585180-52585330	WI-38	lung:	n/a	n/a
2	MAX	chr13:52585193-52586618	H1-hESC	embryonic stem cell:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
3	CTCF	chr13:52585300-52585450	WI-38	lung:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
4	CTCF	chr13:52585300-52585450	GM12865	blood:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
5	CTCF	chr13:52585260-52585410	HCPEpiC	choroid plexus:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
6	CTCF	chr13:52585283-52585388	SK-N-SH_RA	brain:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
7	CTCF	chr13:52585103-52585502	K562	blood:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
8	CTCF	chr13:52585240-52585390	GM12864	blood:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
9	CTCF	chr13:52585260-52585410	HMEC	breast:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
10	CTCF	chr13:52585280-52585430	HVMF	connective:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
11	E2F6	chr13:52585251-52585552	K562	blood:	n/a	n/a
12	CTCF	chr13:52585240-52585390	AG04449	skin:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
13	POLR2A	chr13:52585282-52586896	HepG2	liver:	n/a	n/a
14	MAX	chr13:52585033-52586745	K562	blood:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
15	CTCF	chr13:52585180-52585330	GM12872	blood:	n/a	n/a
16	MAX	chr13:52585114-52586687	K562	blood:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
17	CTCF	chr13:52585240-52585390	SAEC	small airway:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
18	HMGN3	chr13:52585268-52586527	K562	blood:	n/a	n/a
19	POLR2A	chr13:52585205-52586953	HepG2	liver:	n/a	n/a
20	CTCF	chr13:52585220-52585370	HRPEpiC	eye:	n/a	chr13:52585332-52585341
21	CTCF	chr13:52585300-52585450	HUVEC	blood vessel:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
22	CTCF	chr13:52585240-52585390	HAc	cerebellar:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
23	MXI1	chr13:52585254-52586927	HepG2	liver:	n/a	n/a
24	CTCF	chr13:52585240-52585390	HEK293	kidney:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
25	CTCF	chr13:52585282-52585444	K562	blood:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
26	CTCF	chr13:52585220-52585370	HMF	breast:	n/a	chr13:52585332-52585341
27	MAZ	chr13:52585291-52585491	HepG2	liver:	n/a	n/a
28	CTCF	chr13:52585220-52585370	BJ	skin:	n/a	chr13:52585332-52585341
29	MAX	chr13:52585307-52586999	NB4	blood:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
30	MYC	chr13:52585302-52586719	K562	blood:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
31	CTCF	chr13:52585260-52585410	HAc	cerebellar:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
32	MAX	chr13:52585242-52586640	ECC-1	luminal epithelium:	n/a	chr13:52585522-52585533 chr13:52586465-52586475 chr13:52586074-52586084 chr13:52586244-52586254
33	CTCF	chr13:52585240-52585390	AG09309	skin:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
34	JUND	chr13:52585233-52585766	H1-hESC	embryonic stem cell:	n/a	n/a
35	RAD21	chr13:52585200-52585578	HepG2	liver:	n/a	n/a
36	SMC3	chr13:52585306-52585347	K562	blood:	n/a	n/a
37	CTCF	chr13:52585217-52585469	K562	blood:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
38	CTCF	chr13:52585300-52585450	HPF	lung:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
39	POLR2A	chr13:52585203-52586920	K562	blood:	n/a	n/a
40	CTCF	chr13:52585240-52585390	AG10803	skin:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
41	ZBTB7A	chr13:52585216-52586411	K562	blood:	n/a	chr13:52585632-52585639
42	CTCF	chr13:52585240-52585390	AoAF	blood vessel:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
43	CTCF	chr13:52585240-52585390	HMEC	breast:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
44	CTCF	chr13:52585260-52585410	K562	blood:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
45	CTCF	chr13:52585198-52585484	IMR90	lung:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
46	CTCF	chr13:52585220-52585370	K562	blood:	n/a	chr13:52585332-52585341
47	UBTF	chr13:52585288-52586064	K562	blood:	n/a	n/a
48	CTCF	chr13:52585280-52585430	SAEC	small airway:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
49	CTCF	chr13:52585260-52585410	HBMEC	blood vessel:	n/a	chr13:52585373-52585382 chr13:52585332-52585341
50	CTCF	chr13:52585280-52585430	NHEK	skin:	n/a	chr13:52585373-52585382 chr13:52585332-52585341

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:52585283-52585333	K562	blood:	n/a
2	chr13:52585283-52585333	HRPEpiC	eye:	n/a
3	chr13:52585283-52585333	HepG2	liver:	n/a
4	chr13:52585283-52585333	PANC-1	pancreas:	n/a
5	chr13:52585283-52585333	HMEC	breast:	n/a
6	chr13:52585283-52585333	RPTEC	kidney:	n/a
7	chr13:52585283-52585333	LNCaP	prostate:	n/a
8	chr13:52585283-52585333	AG09309	skin:	n/a
9	chr13:52585283-52585333	HCF	heart:	n/a
10	chr13:52585283-52585333	NHBE	bronchial:	n/a
11	chr13:52585283-52585333	NB4	blood:	n/a
12	chr13:52585283-52585333	ProgFib	skin:	n/a
13	chr13:52585283-52585333	HAEpiC	amniotic membrane:	n/a
14	chr13:52585283-52585333	GM19239	blood:	n/a
15	chr13:52585283-52585333	HUVEC	blood vessel:	n/a
16	chr13:52585283-52585333	U87	brain:	n/a
17	chr13:52585283-52585333	BE2_C	brain:	n/a
18	chr13:52585283-52585333	NHDF-neo	bronchial:	n/a
19	chr13:52585283-52585333	SK-N-MC	brain:	n/a
20	chr13:52585283-52585333	HCT-116	colon:	n/a
21	chr13:52585283-52585333	SKMC	muscle:	n/a
22	chr13:52585283-52585333	HIPEpiC	eye:	n/a
23	chr13:52585283-52585333	AoSMC	blood vessel:	n/a
24	chr13:52585283-52585333	SK-N-SH_RA	brain:	n/a
25	chr13:52585283-52585333	HRE	kidney:	n/a
26	chr13:52585283-52585333	HPAEpiC	pulmonary alveolar:	n/a
27	chr13:52585283-52585333	HEK293	kidney:	embryo
28	chr13:52585283-52585333	GM12891	blood:	n/a
29	chr13:52585283-52585333	HRCEpiC	kidney:	n/a
30	chr13:52585283-52585333	Caco-2	colon:	n/a
31	chr13:52585283-52585333	T-47D	breast:	n/a
32	chr13:52585283-52585333	MCF10A-Er-Src	breast:	n/a
33	chr13:52585283-52585333	GM06990	blood:	n/a
34	chr13:52585283-52585333	ovcar-3	ovarian:	n/a
35	chr13:52585283-52585333	HCM	heart:	n/a
36	chr13:52585283-52585333	HEEpiC	esophagus:	n/a
37	chr13:52585283-52585333	ECC-1	luminal epithelium:	n/a
38	chr13:52585283-52585333	Hela-S3	cervix:	n/a
39	chr13:52585283-52585333	AG04450	lung:	fetal
40	chr13:52585283-52585333	NH-A	brain:	n/a
41	chr13:52585283-52585333	HL-60	blood:	n/a
42	chr13:52585283-52585333	MCF-7	breast:	n/a
43	chr13:52585283-52585333	Jurkat	blood:	n/a
44	chr13:52585283-52585333	AG04449	skin:	fetal
45	chr13:52585283-52585333	GM12878	blood:	n/a
46	chr13:52585283-52585333	AG09319	gingival:	n/a
47	chr13:52585283-52585333	H1-hESC	embryonic stem cell:	embryo
48	chr13:52585283-52585333	BJ	skin:	n/a
49	chr13:52585283-52585333	HNPCEpiC	eye:	n/a
50	chr13:52585283-52585333	NT2-D1	testis:	n/a

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

Variant related genes	Relation type
ALG11	TF binding region
ALG11	CpG island
ENSG00000197168	Chromatin interaction
ENSG00000253710	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000253797	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1122934	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4091568	1.00[ASN][1000 genomes]
rs4941729	1.00[ASN][1000 genomes]
rs55667430	0.87[ASN][1000 genomes]
rs55715265	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57345934	1.00[ASN][1000 genomes]
rs61957231	1.00[ASN][1000 genomes]
rs61957232	1.00[ASN][1000 genomes]
rs61957233	1.00[ASN][1000 genomes]
rs61957238	1.00[ASN][1000 genomes]
rs61957248	1.00[ASN][1000 genomes]
rs61957249	1.00[ASN][1000 genomes]
rs61957252	1.00[ASN][1000 genomes]
rs61957253	1.00[ASN][1000 genomes]
rs61957254	1.00[ASN][1000 genomes]
rs61957255	1.00[ASN][1000 genomes]
rs61957256	1.00[ASN][1000 genomes]
rs61957258	1.00[ASN][1000 genomes]
rs61957297	1.00[ASN][1000 genomes]
rs61958782	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958784	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958800	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958801	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958802	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958803	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958806	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958807	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958860	1.00[ASN][1000 genomes]
rs61958863	1.00[ASN][1000 genomes]
rs61958865	1.00[ASN][1000 genomes]
rs719349	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7333070	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73502305	1.00[ASN][1000 genomes]
rs73502307	1.00[ASN][1000 genomes]
rs9526818	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526840	1.00[ASN][1000 genomes]
rs9535814	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535818	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535831	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535838	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535839	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535850	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535852	1.00[ASN][1000 genomes]
rs9535859	1.00[ASN][1000 genomes]
rs9535869	1.00[ASN][1000 genomes]
rs9535870	1.00[ASN][1000 genomes]
rs9535875	1.00[ASN][1000 genomes]
rs9535881	1.00[ASN][1000 genomes]
rs9535886	1.00[ASN][1000 genomes]
rs9535890	1.00[ASN][1000 genomes]
rs9535892	1.00[ASN][1000 genomes]
rs9535893	1.00[ASN][1000 genomes]
rs9535894	1.00[ASN][1000 genomes]
rs9535897	1.00[ASN][1000 genomes]
rs9535900	1.00[ASN][1000 genomes]
rs9535901	1.00[ASN][1000 genomes]
rs9535902	1.00[ASN][1000 genomes]
rs9535903	1.00[ASN][1000 genomes]
rs9535906	1.00[ASN][1000 genomes]
rs9535909	1.00[ASN][1000 genomes]
rs9535910	1.00[ASN][1000 genomes]
rs9535911	1.00[ASN][1000 genomes]
rs9535913	1.00[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

No data

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	chr13:52584200-52585600	Flanking Active TSS	Liver	Liver
3	chr13:52584200-52585800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr13:52584400-52585400	Active TSS	HepG2	liver
5	chr13:52584400-52585600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr13:52584400-52587200	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr13:52584400-52587400	Active TSS	Brain Anterior Caudate	brain
8	chr13:52584400-52587400	Active TSS	Right Ventricle	heart
9	chr13:52584400-52587600	Active TSS	Right Atrium	heart
10	chr13:52584400-52587800	Active TSS	Brain Angular Gyrus	brain
11	chr13:52584600-52585400	Flanking Active TSS	Fetal Lung	lung
12	chr13:52584600-52585600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr13:52584600-52587400	Active TSS	Stomach Smooth Muscle	stomach
14	chr13:52584600-52587800	Active TSS	Fetal Brain Female	brain
15	chr13:52584800-52585400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:52584800-52585400	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr13:52584800-52585400	Flanking Active TSS	Brain Substantia Nigra	brain
18	chr13:52584800-52586000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr13:52584800-52586000	Active TSS	Fetal Brain Male	brain
20	chr13:52584800-52587600	Active TSS	NHDF-Ad	bronchial
21	chr13:52584800-52588000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr13:52584800-52588000	Active TSS	K562	blood
23	chr13:52585000-52585400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr13:52585000-52585400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:52585000-52585400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr13:52585000-52585400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr13:52585000-52585400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
28	chr13:52585000-52585400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
29	chr13:52585000-52585400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
30	chr13:52585000-52585400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr13:52585000-52585400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr13:52585000-52585400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr13:52585000-52585400	Flanking Active TSS	Colon Smooth Muscle	Colon
34	chr13:52585000-52585400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
35	chr13:52585000-52585400	Flanking Active TSS	Fetal Stomach	stomach
36	chr13:52585000-52585400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
37	chr13:52585000-52585400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr13:52585000-52585400	Flanking Active TSS	HSMMtube	muscle
39	chr13:52585000-52585400	Flanking Bivalent TSS/Enh	NH-A	brain
40	chr13:52585000-52585600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
41	chr13:52585000-52585600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr13:52585000-52585600	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr13:52585000-52585600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr13:52585000-52585600	Flanking Active TSS	HMEC	breast
45	chr13:52585000-52585800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
46	chr13:52585000-52585800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
47	chr13:52585000-52585800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr13:52585000-52586000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr13:52585000-52586000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
50	chr13:52585000-52586000	Bivalent/Poised TSS	Thymus	Thymus

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