Variant report

Variant	rs55860060
Chromosome Location	chr13:39260893-39260894
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	SP1	chr13:39260679-39261399	H1-hESC	embryonic stem cell:	n/a	chr13:39261037-39261046 chr13:39261030-39261041 chr13:39260835-39260849
2	POLR2A	chr13:39260776-39261499	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr13:39260573-39260933	H1-hESC	embryonic stem cell:	n/a	chr13:39260834-39260843 chr13:39260638-39260649
4	POLR2A	chr13:39260409-39261686	ECC-1	luminal epithelium:	n/a	n/a
5	CHD2	chr13:39260502-39262120	H1-hESC	embryonic stem cell:	n/a	chr13:39261114-39261124
6	MXI1	chr13:39260671-39261714	H1-hESC	embryonic stem cell:	n/a	n/a
7	ATF2	chr13:39260843-39261365	H1-hESC	embryonic stem cell:	n/a	n/a
8	TBP	chr13:39260348-39262065	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr13:39260839-39261076	H1-hESC	embryonic stem cell:	n/a	n/a
10	CREB1	chr13:39260492-39261483	H1-hESC	embryonic stem cell:	n/a	n/a
11	JUND	chr13:39260851-39261416	H1-hESC	embryonic stem cell:	n/a	chr13:39261073-39261082
12	SP1	chr13:39260856-39261309	H1-hESC	embryonic stem cell:	n/a	chr13:39261037-39261046 chr13:39261030-39261041
13	CHD1	chr13:39260721-39261618	H1-hESC	embryonic stem cell:	n/a	chr13:39261114-39261124
14	POLR2A	chr13:39260842-39261548	MCF-7	breast:	n/a	n/a
15	E2F4	chr13:39260619-39261253	MCF10A-Er-Src	breast:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
16	GTF2F1	chr13:39260601-39261588	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr13:39260206-39261986	ECC-1	luminal epithelium:	n/a	chr13:39260787-39260796
18	TCF12	chr13:39260846-39261386	ECC-1	luminal epithelium:	n/a	chr13:39261108-39261115
19	STAT3	chr13:39260893-39261010	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr13:39260772-39261448	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3AK20	chr13:39260053-39260966	MCF-7	breast:	n/a	n/a
22	SIN3A	chr13:39260139-39262313	H1-hESC	embryonic stem cell:	n/a	chr13:39261307-39261320
23	TAF1	chr13:39260763-39261599	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr13:39260556-39261638	H1-hESC	embryonic stem cell:	n/a	n/a
25	SIN3AK20	chr13:39259931-39261825	MCF-7	breast:	n/a	n/a
26	TAF1	chr13:39260458-39261731	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr13:39260091-39261370	MCF-7	breast:	n/a	chr13:39260787-39260796
28	SP2	chr13:39260851-39261281	H1-hESC	embryonic stem cell:	n/a	n/a
29	SETDB1	chr13:39260078-39261495	U2OS	brain:	n/a	n/a
30	POLR2A	chr13:39260314-39262185	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr13:39260515-39261439	H1-hESC	embryonic stem cell:	n/a	chr13:39260834-39260843 chr13:39261291-39261302 chr13:39261309-39261323 chr13:39260638-39260649 chr13:39261294-39261308
32	ZNF143	chr13:39260139-39262011	H1-hESC	embryonic stem cell:	n/a	chr13:39261180-39261198 chr13:39261345-39261355
33	PML	chr13:39260825-39261455	MCF-7	breast:	n/a	chr13:39261405-39261413
34	MAX	chr13:39260345-39262000	ECC-1	luminal epithelium:	n/a	chr13:39260787-39260796
35	E2F6	chr13:39260491-39262274	H1-hESC	embryonic stem cell:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
36	MAX	chr13:39260171-39261492	H1-hESC	embryonic stem cell:	n/a	chr13:39260787-39260796
37	TAF1	chr13:39260745-39261601	ECC-1	luminal epithelium:	n/a	n/a
38	GATA3	chr13:39260857-39262108	MCF-7	breast:	n/a	n/a
39	KAP1	chr13:39260290-39261341	U2OS	brain:	n/a	n/a
40	E2F6	chr13:39260737-39262112	H1-hESC	embryonic stem cell:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
41	MYC	chr13:39260893-39261278	H1-hESC	embryonic stem cell:	n/a	n/a
42	TCF12	chr13:39260808-39261281	ECC-1	luminal epithelium:	n/a	chr13:39261108-39261115
43	TEAD4	chr13:39260772-39261428	H1-hESC	embryonic stem cell:	n/a	n/a
44	ZNF263	chr13:39260638-39262432	HEK293-T-REx	kidney:	n/a	chr13:39261113-39261122 chr13:39261031-39261040
45	MAX	chr13:39260086-39261151	MCF-7	breast:	n/a	chr13:39260787-39260796
46	RAD21	chr13:39260063-39261429	H1-hESC	embryonic stem cell:	n/a	n/a
47	SP4	chr13:39260789-39261588	H1-hESC	embryonic stem cell:	n/a	chr13:39260840-39260856 chr13:39261030-39261041
48	CTBP2	chr13:39260245-39262457	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr13:39260814-39261466	H1-hESC	embryonic stem cell:	n/a	n/a
50	ZBTB7A	chr13:39260860-39261885	ECC-1	luminal epithelium:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:39260877-39260927	ECC-1	luminal epithelium:	n/a
2	chr13:39260874-39260924	NT2-D1	testis:	n/a
3	chr13:39260877-39260927	NHDF-neo	bronchial:	n/a
4	chr13:39260874-39260924	AG09319	gingival:	n/a
5	chr13:39260874-39260924	HPAEpiC	pulmonary alveolar:	n/a
6	chr13:39260874-39260924	HMEC	breast:	n/a
7	chr13:39260877-39260927	SK-N-SH	brain:	n/a
8	chr13:39260874-39260924	NHDF-neo	bronchial:	n/a
9	chr13:39260874-39260924	MCF10A-Er-Src	breast:	n/a
10	chr13:39260874-39260924	PFSK-1	brain:	n/a
11	chr13:39260874-39260924	HAEpiC	amniotic membrane:	n/a
12	chr13:39260877-39260927	SK-N-SH_RA	brain:	n/a
13	chr13:39260874-39260924	AG04450	lung:	fetal
14	chr13:39260877-39260927	NB4	blood:	n/a
15	chr13:39260874-39260924	HEEpiC	esophagus:	n/a
16	chr13:39260874-39260924	SK-N-MC	brain:	n/a
17	chr13:39260874-39260924	AG04449	skin:	fetal
18	chr13:39260874-39260924	Caco-2	colon:	n/a
19	chr13:39260877-39260927	HAEpiC	amniotic membrane:	n/a
20	chr13:39260877-39260927	HCT-116	colon:	n/a
21	chr13:39260874-39260924	MCF-7	breast:	n/a
22	chr13:39260874-39260924	LNCaP	prostate:	n/a
23	chr13:39260874-39260924	HEK293	kidney:	embryo
24	chr13:39260874-39260924	ovcar-3	ovarian:	n/a
25	chr13:39260874-39260924	NHBE	bronchial:	n/a
26	chr13:39260874-39260924	SK-N-SH	brain:	n/a
27	chr13:39260874-39260924	K562	blood:	n/a
28	chr13:39260874-39260924	GM06990	blood:	n/a
29	chr13:39260874-39260924	ProgFib	skin:	n/a
30	chr13:39260877-39260927	BE2_C	brain:	n/a
31	chr13:39260874-39260924	GM12878	blood:	n/a
32	chr13:39260874-39260924	AG10803	skin:	n/a
33	chr13:39260874-39260924	NB4	blood:	n/a
34	chr13:39260877-39260927	NHBE	bronchial:	n/a
35	chr13:39260874-39260924	HepG2	liver:	n/a
36	chr13:39260877-39260927	H1-hESC	embryonic stem cell:	embryo
37	chr13:39260874-39260924	SK-N-SH_RA	brain:	n/a
38	chr13:39260874-39260924	AG09309	skin:	n/a
39	chr13:39260877-39260927	PFSK-1	brain:	n/a
40	chr13:39260874-39260924	U87	brain:	n/a
41	chr13:39260874-39260924	BE2_C	brain:	n/a
42	chr13:39260874-39260924	PrEC	prostate:	n/a
43	chr13:39260877-39260927	A549	lung:	n/a
44	chr13:39260874-39260924	HL-60	blood:	n/a
45	chr13:39260877-39260927	HRE	kidney:	n/a
46	chr13:39260877-39260927	SKMC	muscle:	n/a
47	chr13:39260874-39260924	H1-hESC	embryonic stem cell:	embryo
48	chr13:39260874-39260924	IMR90	lung:	fetal
49	chr13:39260877-39260927	IMR90	lung:	fetal
50	chr13:39260877-39260927	HEEpiC	esophagus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:39256386..39258055-chr13:39258985..39261054,2	MCF-7	breast:
2	chr13:39260551..39262193-chr6:28047138..28049723,2	MCF-7	breast:
3	chr13:39251483..39253844-chr13:39259100..39260979,2	MCF-7	breast:
4	chr13:39259930..39261837-chr13:39400225..39402249,2	MCF-7	breast:
5	chr13:39259553..39261802-chr13:39611603..39613271,2	MCF-7	breast:
6	chr13:39255037..39256959-chr13:39258816..39261083,2	MCF-7	breast:

Variant related genes	Relation type
FREM2	TF binding region
FREM2	CpG island
ENSG00000188811	Chromatin interaction
ENSG00000120685	Chromatin interaction
ENSG00000225350	Chromatin interaction
ENSG00000197279	Chromatin interaction
ENSG00000272009	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11147723	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11147724	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11147725	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17244358	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2053848	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2122208	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2122212	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2197879	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442335	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442339	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442340	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2442341	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442343	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2442344	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2442373	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2442379	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2496418	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2496419	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2496420	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2496425	0.95[EUR][1000 genomes]
rs2496430	0.85[AMR][1000 genomes]
rs2496433	0.83[AMR][1000 genomes]
rs35378642	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4329795	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55880170	0.83[AMR][1000 genomes]
rs55922882	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6563629	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7331440	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7991701	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs895895	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs930659	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs930660	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9566354	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9576589	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576590	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576591	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576592	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576595	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9634754	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9788341	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832584	chr13:39074265-39284724	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv832585	chr13:39233307-39424375	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39259600-39261800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr13:39259600-39262000	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr13:39259800-39261400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr13:39259800-39262000	Active TSS	Fetal Kidney	kidney
5	chr13:39260000-39261000	Active TSS	Fetal Intestine Large	intestine
6	chr13:39260000-39261600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr13:39260000-39261600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr13:39260000-39261800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr13:39260000-39261800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:39260000-39261800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr13:39260000-39261800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr13:39260000-39261800	Active TSS	Aorta	Aorta
13	chr13:39260000-39262000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr13:39260000-39262000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:39260000-39262000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr13:39260000-39262200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr13:39260000-39262200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:39260000-39262200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr13:39260200-39261200	Active TSS	Brain Cingulate Gyrus	brain
20	chr13:39260200-39261400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr13:39260200-39261400	Active TSS	Ovary	ovary
22	chr13:39260200-39261400	Active TSS	Right Ventricle	heart
23	chr13:39260200-39261600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
24	chr13:39260200-39261600	Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr13:39260200-39261800	Flanking Active TSS	Liver	Liver
26	chr13:39260200-39261800	Active TSS	Brain Hippocampus Middle	brain
27	chr13:39260200-39262000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr13:39260200-39262000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr13:39260200-39262000	Active TSS	Fetal Heart	heart
30	chr13:39260200-39262000	Active TSS	Psoas Muscle	Psoas
31	chr13:39260200-39262200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr13:39260200-39262200	Active TSS	Brain Angular Gyrus	brain
33	chr13:39260200-39262200	Active TSS	Brain Substantia Nigra	brain
34	chr13:39260200-39262200	Active TSS	Rectal Smooth Muscle	rectum
35	chr13:39260200-39262200	Active TSS	Right Atrium	heart
36	chr13:39260200-39262400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:39260200-39262400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr13:39260200-39262400	Active TSS	Brain Anterior Caudate	brain
39	chr13:39260200-39262400	Active TSS	Colon Smooth Muscle	Colon
40	chr13:39260400-39261000	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr13:39260400-39261000	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
42	chr13:39260400-39261200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
43	chr13:39260400-39261400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr13:39260400-39261400	Active TSS	Colonic Mucosa	Colon
45	chr13:39260400-39261400	Active TSS	Pancreas	Pancrea
46	chr13:39260400-39261400	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr13:39260400-39261800	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr13:39260400-39261800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
49	chr13:39260400-39261800	Active TSS	Gastric	stomach
50	chr13:39260400-39261800	Active TSS	Left Ventricle	heart

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