Variant report

Variant	rs2496421
Chromosome Location	chr13:39261047-39261048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:73)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:73 , 50 per page) page: 1 2

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	POLR2A	chr13:39260409-39261686	ECC-1	luminal epithelium:	n/a	n/a
4	CHD2	chr13:39260502-39262120	H1-hESC	embryonic stem cell:	n/a	chr13:39261114-39261124
5	RAD21	chr13:39260922-39261437	H1-hESC	embryonic stem cell:	n/a	n/a
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	NFYB	chr13:39260986-39261283	K562	blood:	n/a	chr13:39261073-39261086
11	CREB1	chr13:39260492-39261483	H1-hESC	embryonic stem cell:	n/a	n/a
12	JUND	chr13:39260851-39261416	H1-hESC	embryonic stem cell:	n/a	chr13:39261073-39261082
13	NFYA	chr13:39261030-39261180	GM12878	blood:	n/a	chr13:39261073-39261086
14	SP1	chr13:39260856-39261309	H1-hESC	embryonic stem cell:	n/a	chr13:39261037-39261046 chr13:39261030-39261041
15	CHD1	chr13:39260721-39261618	H1-hESC	embryonic stem cell:	n/a	chr13:39261114-39261124
16	USF2	chr13:39260995-39261309	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr13:39260842-39261548	MCF-7	breast:	n/a	n/a
18	E2F4	chr13:39260619-39261253	MCF10A-Er-Src	breast:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
19	GTF2F1	chr13:39260601-39261588	H1-hESC	embryonic stem cell:	n/a	n/a
20	MAX	chr13:39260206-39261986	ECC-1	luminal epithelium:	n/a	chr13:39260787-39260796
21	ATF2	chr13:39260938-39261357	H1-hESC	embryonic stem cell:	n/a	n/a
22	TCF12	chr13:39260846-39261386	ECC-1	luminal epithelium:	n/a	chr13:39261108-39261115
23	POLR2A	chr13:39260772-39261448	H1-hESC	embryonic stem cell:	n/a	n/a
24	TEAD4	chr13:39260942-39261381	H1-hESC	embryonic stem cell:	n/a	n/a
25	SIN3A	chr13:39260139-39262313	H1-hESC	embryonic stem cell:	n/a	chr13:39261307-39261320
26	TAF1	chr13:39260763-39261599	ECC-1	luminal epithelium:	n/a	n/a
27	POLR2A	chr13:39260556-39261638	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3AK20	chr13:39259931-39261825	MCF-7	breast:	n/a	n/a
29	TAF1	chr13:39260458-39261731	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr13:39260091-39261370	MCF-7	breast:	n/a	chr13:39260787-39260796
31	SP2	chr13:39260851-39261281	H1-hESC	embryonic stem cell:	n/a	n/a
32	SP2	chr13:39260895-39261387	H1-hESC	embryonic stem cell:	n/a	n/a
33	SP4	chr13:39260990-39261370	H1-hESC	embryonic stem cell:	n/a	chr13:39261030-39261041
34	SETDB1	chr13:39260078-39261495	U2OS	brain:	n/a	n/a
35	POLR2A	chr13:39260314-39262185	H1-hESC	embryonic stem cell:	n/a	n/a
36	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
37	ZNF143	chr13:39260139-39262011	H1-hESC	embryonic stem cell:	n/a	chr13:39261180-39261198 chr13:39261345-39261355
38	NFYB	chr13:39260921-39261300	GM12878	blood:	n/a	chr13:39261073-39261086
39	NANOG	chr13:39261047-39261288	H1-hESC	embryonic stem cell:	n/a	n/a
40	PML	chr13:39260825-39261455	MCF-7	breast:	n/a	chr13:39261405-39261413
41	MYC	chr13:39260976-39261063	MCF10A-Er-Src	breast:	n/a	n/a
42	MAX	chr13:39260345-39262000	ECC-1	luminal epithelium:	n/a	chr13:39260787-39260796
43	E2F6	chr13:39260491-39262274	H1-hESC	embryonic stem cell:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
44	MAX	chr13:39260171-39261492	H1-hESC	embryonic stem cell:	n/a	chr13:39260787-39260796
45	TAF1	chr13:39260745-39261601	ECC-1	luminal epithelium:	n/a	n/a
46	GATA3	chr13:39260857-39262108	MCF-7	breast:	n/a	n/a
47	KAP1	chr13:39260290-39261341	U2OS	brain:	n/a	n/a
48	PBX3	chr13:39260978-39261338	SK-N-SH	brain:	n/a	chr13:39261075-39261084
49	E2F6	chr13:39260737-39262112	H1-hESC	embryonic stem cell:	n/a	chr13:39261047-39261061 chr13:39261046-39261061
50	MYC	chr13:39260893-39261278	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:39261045-39261095	SAEC	small airway:	n/a
2	chr13:39261045-39261095	HL-60	blood:	n/a
3	chr13:39261045-39261095	BE2_C	brain:	n/a
4	chr13:39261045-39261095	Hela-S3	cervix:	n/a
5	chr13:39261045-39261095	NT2-D1	testis:	n/a
6	chr13:39261045-39261095	NH-A	brain:	n/a
7	chr13:39261045-39261095	HCT-116	colon:	n/a
8	chr13:39261045-39261095	GM19239	blood:	n/a
9	chr13:39261045-39261095	HEEpiC	esophagus:	n/a
10	chr13:39261045-39261095	LNCaP	prostate:	n/a
11	chr13:39261045-39261095	HRPEpiC	eye:	n/a
12	chr13:39261045-39261095	HNPCEpiC	eye:	n/a
13	chr13:39261045-39261095	GM12878	blood:	n/a
14	chr13:39261045-39261095	HCF	heart:	n/a
15	chr13:39261045-39261095	AG10803	skin:	n/a
16	chr13:39261045-39261095	T-47D	breast:	n/a
17	chr13:39261045-39261095	NB4	blood:	n/a
18	chr13:39261045-39261095	Hepatocyte	liver:	n/a
19	chr13:39261045-39261095	GM06990	blood:	n/a
20	chr13:39261045-39261095	BJ	skin:	n/a
21	chr13:39261045-39261095	HAEpiC	amniotic membrane:	n/a
22	chr13:39261045-39261095	HCM	heart:	n/a
23	chr13:39261045-39261095	GM12892	blood:	n/a
24	chr13:39261045-39261095	NHBE	bronchial:	n/a
25	chr13:39261045-39261095	MCF10A-Er-Src	breast:	n/a
26	chr13:39261045-39261095	ovcar-3	ovarian:	n/a
27	chr13:39261045-39261095	HUVEC	blood vessel:	n/a
28	chr13:39261045-39261095	ECC-1	luminal epithelium:	n/a
29	chr13:39261045-39261095	Caco-2	colon:	n/a
30	chr13:39261045-39261095	Jurkat	blood:	n/a
31	chr13:39261045-39261095	PANC-1	pancreas:	n/a
32	chr13:39261045-39261095	HRE	kidney:	n/a
33	chr13:39261045-39261095	HRCEpiC	kidney:	n/a
34	chr13:39261045-39261095	SK-N-SH_RA	brain:	n/a
35	chr13:39261045-39261095	HepG2	liver:	n/a
36	chr13:39261045-39261095	HPAEpiC	pulmonary alveolar:	n/a
37	chr13:39261045-39261095	H1-hESC	embryonic stem cell:	embryo
38	chr13:39261045-39261095	SK-N-MC	brain:	n/a
39	chr13:39261045-39261095	AoSMC	blood vessel:	n/a
40	chr13:39261045-39261095	HMEC	breast:	n/a
41	chr13:39261045-39261095	AG04450	lung:	fetal
42	chr13:39261045-39261095	PrEC	prostate:	n/a
43	chr13:39261045-39261095	NHDF-neo	bronchial:	n/a
44	chr13:39261045-39261095	IMR90	lung:	fetal
45	chr13:39261045-39261095	A549	lung:	n/a
46	chr13:39261045-39261095	MCF-7	breast:	n/a
47	chr13:39261045-39261095	HEK293	kidney:	embryo
48	chr13:39261045-39261095	AG09319	gingival:	n/a
49	chr13:39261045-39261095	GM12891	blood:	n/a
50	chr13:39261045-39261095	AG09309	skin:	n/a

(count:5 , 50 per page) page: 1

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	chr13:39259930..39261837-chr13:39400225..39402249,2	MCF-7	breast:
4	chr13:39259553..39261802-chr13:39611603..39613271,2	MCF-7	breast:
5	chr13:39255037..39256959-chr13:39258816..39261083,2	MCF-7	breast:

No data

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

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs2442331	1.00[EUR][1000 genomes]
rs2442332	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2442333	1.00[EUR][1000 genomes]
rs2442334	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2442336	1.00[EUR][1000 genomes]
rs2442345	1.00[EUR][1000 genomes]
rs2442346	1.00[EUR][1000 genomes]
rs2442360	1.00[EUR][1000 genomes]
rs2442366	1.00[EUR][1000 genomes]
rs2442371	1.00[EUR][1000 genomes]
rs2442372	1.00[EUR][1000 genomes]
rs2442374	1.00[EUR][1000 genomes]
rs2442376	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2442378	1.00[EUR][1000 genomes]
rs2442380	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2496398	1.00[EUR][1000 genomes]
rs2496403	1.00[EUR][1000 genomes]
rs2496411	1.00[EUR][1000 genomes]
rs2496413	1.00[EUR][1000 genomes]
rs2496414	1.00[EUR][1000 genomes]
rs2496424	1.00[EUR][1000 genomes]
rs2496426	1.00[EUR][1000 genomes]
rs2496428	1.00[AMR][1000 genomes]
rs2496432	1.00[EUR][1000 genomes]
rs2496447	1.00[EUR][1000 genomes]
rs2595557	1.00[EUR][1000 genomes]
rs2595559	1.00[EUR][1000 genomes]
rs2595562	1.00[EUR][1000 genomes]
rs2595567	1.00[EUR][1000 genomes]
rs2805082	1.00[EUR][1000 genomes]
rs2805083	1.00[EUR][1000 genomes]
rs2805084	1.00[EUR][1000 genomes]
rs2805085	1.00[EUR][1000 genomes]
rs2805089	1.00[EUR][1000 genomes]
rs7320346	1.00[EUR][1000 genomes]
rs7325603	1.00[AMR][1000 genomes]
rs7991794	1.00[AMR][1000 genomes]
rs9315610	0.83[AMR][1000 genomes]
rs9603410	1.00[AMR][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:99 , 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	chr13:39260000-39261600	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr13:39260000-39261600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr13:39260000-39261800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr13:39260000-39261800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:39260000-39261800	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr13:39260000-39261800	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr13:39260000-39261800	Active TSS	Aorta	Aorta
12	chr13:39260000-39262000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr13:39260000-39262000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:39260000-39262000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr13:39260000-39262200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr13:39260000-39262200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr13:39260000-39262200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:39260200-39261200	Active TSS	Brain Cingulate Gyrus	brain
19	chr13:39260200-39261400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr13:39260200-39261400	Active TSS	Ovary	ovary
21	chr13:39260200-39261400	Active TSS	Right Ventricle	heart
22	chr13:39260200-39261600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
23	chr13:39260200-39261600	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr13:39260200-39261800	Flanking Active TSS	Liver	Liver
25	chr13:39260200-39261800	Active TSS	Brain Hippocampus Middle	brain
26	chr13:39260200-39262000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr13:39260200-39262000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:39260200-39262000	Active TSS	Fetal Heart	heart
29	chr13:39260200-39262000	Active TSS	Psoas Muscle	Psoas
30	chr13:39260200-39262200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr13:39260200-39262200	Active TSS	Brain Angular Gyrus	brain
32	chr13:39260200-39262200	Active TSS	Brain Substantia Nigra	brain
33	chr13:39260200-39262200	Active TSS	Rectal Smooth Muscle	rectum
34	chr13:39260200-39262200	Active TSS	Right Atrium	heart
35	chr13:39260200-39262400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:39260200-39262400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr13:39260200-39262400	Active TSS	Brain Anterior Caudate	brain
38	chr13:39260200-39262400	Active TSS	Colon Smooth Muscle	Colon
39	chr13:39260400-39261200	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
40	chr13:39260400-39261400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr13:39260400-39261400	Active TSS	Colonic Mucosa	Colon
42	chr13:39260400-39261400	Active TSS	Pancreas	Pancrea
43	chr13:39260400-39261400	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr13:39260400-39261800	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr13:39260400-39261800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
46	chr13:39260400-39261800	Active TSS	Gastric	stomach
47	chr13:39260400-39261800	Active TSS	Left Ventricle	heart
48	chr13:39260400-39262000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
49	chr13:39260400-39262200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr13:39260400-39262200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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