Variant report

Variant	rs60444690
Chromosome Location	chr17:45401414-45401415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:436)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:436 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:45401320-45401470	BJ	skin:	n/a	n/a
2	CTCF	chr17:45401300-45401450	AG04449	skin:	n/a	n/a
3	SP4	chr17:45400936-45401794	H1-hESC	embryonic stem cell:	n/a	chr17:45401272-45401283
4	CTCF	chr17:45401279-45401455	MCF-7	breast:	n/a	n/a
5	REST	chr17:45401028-45401452	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr17:45401001-45402489	GM12891	blood:	n/a	n/a
7	CREB1	chr17:45400695-45401811	HepG2	liver:	n/a	n/a
8	ZBTB7A	chr17:45400618-45401619	K562	blood:	n/a	n/a
9	MAX	chr17:45400728-45402386	A549	lung:	n/a	n/a
10	JUND	chr17:45400812-45401795	A549	lung:	n/a	n/a
11	TEAD4	chr17:45400690-45401520	ECC-1	luminal epithelium:	n/a	n/a
12	GTF2F1	chr17:45401016-45401862	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr17:45400836-45402132	IMR90	lung:	n/a	n/a
14	CTCF	chr17:45401340-45401490	GM12874	blood:	n/a	n/a
15	USF1	chr17:45401142-45401452	HepG2	liver:	n/a	chr17:45401293-45401304
16	POU2F2	chr17:45401169-45401668	GM12878	blood:	n/a	n/a
17	E2F4	chr17:45400687-45401746	MCF10A-Er-Src	breast:	n/a	n/a
18	CTCF	chr17:45401320-45401470	HA-sp	spinal cord:	n/a	n/a
19	ELF1	chr17:45400794-45401880	GM12878	blood:	n/a	n/a
20	SIN3AK20	chr17:45400775-45401661	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr17:45400796-45401741	SK-N-MC	brain:	n/a	n/a
22	MAZ	chr17:45400985-45401901	GM12878	blood:	n/a	n/a
23	MBD4	chr17:45400715-45401772	HepG2	liver:	n/a	n/a
24	MAX	chr17:45400621-45401904	HepG2	liver:	n/a	n/a
25	SETDB1	chr17:45400772-45401848	K562	blood:	n/a	n/a
26	MXI1	chr17:45400898-45401685	HepG2	liver:	n/a	n/a
27	RUNX3	chr17:45400741-45402563	GM12878	blood:	n/a	n/a
28	POLR2A	chr17:45400709-45401762	K562	blood:	n/a	n/a
29	POLR2A	chr17:45400792-45401911	A549	lung:	n/a	n/a
30	USF1	chr17:45400913-45401527	K562	blood:	n/a	chr17:45401293-45401304
31	USF1	chr17:45401025-45401589	SK-N-SH_RA	brain:	n/a	chr17:45401293-45401304
32	MAX	chr17:45400614-45402098	H1-hESC	embryonic stem cell:	n/a	n/a
33	PBX3	chr17:45400790-45402129	A549	lung:	n/a	n/a
34	POLR2A	chr17:45400465-45402245	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr17:45400858-45402457	GM12892	blood:	n/a	n/a
36	NFIC	chr17:45400672-45402561	GM12878	blood:	n/a	n/a
37	MYC	chr17:45400601-45401700	K562	blood:	n/a	n/a
38	CTCF	chr17:45401300-45401450	GM12869	blood:	n/a	n/a
39	USF1	chr17:45400615-45401849	ECC-1	luminal epithelium:	n/a	chr17:45401293-45401304
40	TAF1	chr17:45400989-45401439	SK-N-SH	brain:	n/a	n/a
41	CTCF	chr17:45401061-45401488	GM19240	blood:	n/a	n/a
42	POLR2A	chr17:45400857-45401914	A549	lung:	n/a	n/a
43	CTCF	chr17:45401330-45401469	ProgFib	skin:	n/a	n/a
44	BRCA1	chr17:45401360-45401501	GM12878	blood:	n/a	n/a
45	ELF1	chr17:45400982-45401546	K562	blood:	n/a	n/a
46	CHD2	chr17:45400846-45401729	K562	blood:	n/a	n/a
47	RCOR1	chr17:45400712-45401747	K562	blood:	n/a	n/a
48	RCOR1	chr17:45400911-45401551	HepG2	liver:	n/a	n/a
49	CTCF	chr17:45401320-45401590	HEEpiC	esophagus:	n/a	n/a
50	MXI1	chr17:45400566-45402311	GM12878	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:45401397-45401447	H1-hESC	embryonic stem cell:	embryo
2	chr17:45401397-45401447	NH-A	brain:	n/a
3	chr17:45401397-45401447	HCF	heart:	n/a
4	chr17:45401397-45401447	HL-60	blood:	n/a
5	chr17:45401397-45401447	HRPEpiC	eye:	n/a
6	chr17:45401397-45401447	MCF10A-Er-Src	breast:	n/a
7	chr17:45401397-45401447	GM12891	blood:	n/a
8	chr17:45401397-45401447	HCM	heart:	n/a
9	chr17:45401397-45401447	BE2_C	brain:	n/a
10	chr17:45401397-45401447	HCPEpiC	choroid plexus:	n/a
11	chr17:45401397-45401447	Jurkat	blood:	n/a
12	chr17:45401397-45401447	U87	brain:	n/a
13	chr17:45401397-45401447	HPAEpiC	pulmonary alveolar:	n/a
14	chr17:45401397-45401447	SAEC	small airway:	n/a
15	chr17:45401397-45401447	Hepatocyte	liver:	n/a
16	chr17:45401397-45401447	GM12892	blood:	n/a
17	chr17:45401397-45401447	LNCaP	prostate:	n/a
18	chr17:45401397-45401447	HIPEpiC	eye:	n/a
19	chr17:45401397-45401447	SK-N-SH_RA	brain:	n/a
20	chr17:45401397-45401447	HAEpiC	amniotic membrane:	n/a
21	chr17:45401397-45401447	HEK293	kidney:	embryo
22	chr17:45401397-45401447	CMK	blood:	n/a
23	chr17:45401397-45401447	HRE	kidney:	n/a
24	chr17:45401397-45401447	IMR90	lung:	fetal
25	chr17:45401397-45401447	GM06990	blood:	n/a
26	chr17:45401397-45401447	RPTEC	kidney:	n/a
27	chr17:45401397-45401447	Caco-2	colon:	n/a
28	chr17:45401397-45401447	T-47D	breast:	n/a
29	chr17:45401397-45401447	NT2-D1	testis:	n/a
30	chr17:45401397-45401447	SK-N-SH	brain:	n/a
31	chr17:45401397-45401447	ECC-1	luminal epithelium:	n/a
32	chr17:45401397-45401447	MCF-7	breast:	n/a
33	chr17:45401397-45401447	NHBE	bronchial:	n/a
34	chr17:45401397-45401447	AG10803	skin:	n/a
35	chr17:45401397-45401447	AoSMC	blood vessel:	n/a
36	chr17:45401397-45401447	NHDF-neo	bronchial:	n/a
37	chr17:45401397-45401447	AG04449	skin:	fetal
38	chr17:45401397-45401447	SKMC	muscle:	n/a
39	chr17:45401397-45401447	ProgFib	skin:	n/a
40	chr17:45401397-45401447	SK-N-MC	brain:	n/a
41	chr17:45401397-45401447	AG04450	lung:	fetal
42	chr17:45401397-45401447	BJ	skin:	n/a
43	chr17:45401397-45401447	HEEpiC	esophagus:	n/a
44	chr17:45401397-45401447	PFSK-1	brain:	n/a
45	chr17:45401397-45401447	ovcar-3	ovarian:	n/a
46	chr17:45401397-45401447	HepG2	liver:	n/a
47	chr17:45401397-45401447	AG09319	gingival:	n/a
48	chr17:45401397-45401447	A549	lung:	n/a
49	chr17:45401397-45401447	HCT-116	colon:	n/a
50	chr17:45401397-45401447	GM12878	blood:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45334238..45336850-chr17:45399681..45401766,2	K562	blood:
2	chr17:45234199..45236994-chr17:45399820..45401734,2	MCF-7	breast:
3	chr17:45399600..45403116-chr17:45404916..45409576,7	K562	blood:
4	chr17:45401064..45401883-chr20:30194485..30195180,2	Hela-S3	cervix:
5	chr17:45400573..45401426-chr9:116172200..116173194,2	Hela-S3	cervix:
6	chr17:45143352..45146051-chr17:45399301..45401762,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC040934.1-2	chr17:45400564-45401497	ENSG00000247683
2	lnc-MYL4-4	chr17:45401327-45401440	NONHSAT054299

No data

Variant related genes	Relation type
EFCAB13	TF binding region
ENSG00000263293	TF binding region
EFCAB13	CpG island
ENSG00000263293	CpG island
ENSG00000157653	Chromatin interaction
ENSG00000264395	Chromatin interaction
ENSG00000004897	Chromatin interaction
ENSG00000238419	Chromatin interaction
ENSG00000262879	Chromatin interaction
ENSG00000178852	Chromatin interaction
ENSG00000148229	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs56721370	1.00[AFR][1000 genomes]
rs57044127	1.00[AFR][1000 genomes]
rs57172453	1.00[AFR][1000 genomes]
rs57180192	1.00[AFR][1000 genomes]
rs57216860	1.00[AFR][1000 genomes]
rs59392615	1.00[AFR][1000 genomes]
rs60348832	1.00[AFR][1000 genomes]
rs61274872	0.90[AFR][1000 genomes]
rs73320495	0.90[AFR][1000 genomes]
rs73320498	0.90[AFR][1000 genomes]
rs73322311	0.90[AFR][1000 genomes]
rs73322315	0.90[AFR][1000 genomes]
rs73322322	0.90[AFR][1000 genomes]
rs73322325	1.00[AFR][1000 genomes]
rs73322328	0.91[AFR][1000 genomes]
rs73322329	1.00[AFR][1000 genomes]
rs73322332	1.00[AFR][1000 genomes]
rs73322392	1.00[AFR][1000 genomes]
rs73322393	1.00[AFR][1000 genomes]
rs73322397	1.00[AFR][1000 genomes]
rs73322398	1.00[AFR][1000 genomes]
rs73322400	1.00[AFR][1000 genomes]
rs73324405	1.00[AFR][1000 genomes]
rs73324407	1.00[AFR][1000 genomes]
rs73324416	0.90[AFR][1000 genomes]
rs73324417	0.90[AFR][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	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer 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 miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv962445	chr17:45397004-45428018	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr17:45400000-45402400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr17:45400200-45401600	Active TSS	K562	blood
3	chr17:45400400-45402400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr17:45400400-45402400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr17:45400400-45402400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr17:45400400-45402400	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr17:45400400-45402400	Active TSS	NHLF	lung
8	chr17:45400400-45402600	Active TSS	A549	lung
9	chr17:45400600-45401600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr17:45400600-45401600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr17:45400600-45401600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr17:45400600-45401600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr17:45400600-45401600	Active TSS	Primary T cells fromperipheralblood	blood
14	chr17:45400600-45401600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:45400600-45401600	Bivalent/Poised TSS	NHEK	skin
16	chr17:45400600-45401800	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr17:45400600-45402000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:45400600-45402000	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr17:45400600-45402000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr17:45400600-45402000	Active TSS	Brain Angular Gyrus	brain
21	chr17:45400600-45402000	Active TSS	Pancreas	Pancrea
22	chr17:45400600-45402000	Active TSS	Stomach Mucosa	stomach
23	chr17:45400600-45402000	Flanking Active TSS	NH-A	brain
24	chr17:45400600-45402200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:45400600-45402200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr17:45400600-45402200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:45400600-45402200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr17:45400600-45402200	Active TSS	Brain Cingulate Gyrus	brain
29	chr17:45400600-45402200	Active TSS	Brain Substantia Nigra	brain
30	chr17:45400600-45402200	Active TSS	Colon Smooth Muscle	Colon
31	chr17:45400600-45402200	Active TSS	Fetal Kidney	kidney
32	chr17:45400600-45402200	Active TSS	Left Ventricle	heart
33	chr17:45400600-45402200	Active TSS	Psoas Muscle	Psoas
34	chr17:45400600-45402200	Active TSS	Right Ventricle	heart
35	chr17:45400600-45402400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr17:45400600-45402400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr17:45400600-45402400	Active TSS	Primary T cells from cord blood	blood
38	chr17:45400600-45402400	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr17:45400600-45402400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr17:45400600-45402400	Active TSS	Brain Anterior Caudate	brain
41	chr17:45400600-45402400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
42	chr17:45400600-45402400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr17:45400600-45402400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr17:45400600-45402400	Active TSS	Fetal Intestine Large	intestine
45	chr17:45400600-45402400	Active TSS	Fetal Intestine Small	intestine
46	chr17:45400600-45402400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr17:45400600-45402400	Active TSS	Fetal Muscle Trunk	muscle
48	chr17:45400600-45402400	Active TSS	Ovary	ovary
49	chr17:45400600-45402400	Active TSS	Stomach Smooth Muscle	stomach
50	chr17:45400600-45402400	Active TSS	HSMM	muscle

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