Variant report

Variant	rs58025472
Chromosome Location	chr17:60006022-60006023
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr17:60003695-60006237	Hela-S3	cervix:	n/a	n/a
2	MAX	chr17:60004187-60006067	MCF-7	breast:	n/a	chr17:60005556-60005565
3	SIN3AK20	chr17:60003642-60006145	MCF-7	breast:	n/a	n/a
4	GABPA	chr17:60004352-60006043	MCF-7	breast:	n/a	chr17:60005399-60005410 chr17:60005401-60005410 chr17:60005396-60005410 chr17:60005399-60005413

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:60005984-60006034	HCPEpiC	choroid plexus:	n/a
2	chr17:60005984-60006034	HL-60	blood:	n/a
3	chr17:60005984-60006034	HCT-116	colon:	n/a
4	chr17:60005984-60006034	SK-N-SH	brain:	n/a
5	chr17:60005984-60006034	Caco-2	colon:	n/a
6	chr17:60005984-60006034	HUVEC	blood vessel:	n/a
7	chr17:60005984-60006034	AG09309	skin:	n/a
8	chr17:60005984-60006034	SK-N-SH_RA	brain:	n/a
9	chr17:60005984-60006034	GM19239	blood:	n/a
10	chr17:60005984-60006034	HRE	kidney:	n/a
11	chr17:60005984-60006034	IMR90	lung:	fetal
12	chr17:60005984-60006034	RPTEC	kidney:	n/a
13	chr17:60005984-60006034	NB4	blood:	n/a
14	chr17:60005984-60006034	NHDF-neo	bronchial:	n/a
15	chr17:60005984-60006034	HMEC	breast:	n/a
16	chr17:60005984-60006034	HEK293	kidney:	embryo
17	chr17:60005984-60006034	HRCEpiC	kidney:	n/a
18	chr17:60005984-60006034	NH-A	brain:	n/a
19	chr17:60005984-60006034	HAEpiC	amniotic membrane:	n/a
20	chr17:60005984-60006034	AG10803	skin:	n/a
21	chr17:60005984-60006034	HepG2	liver:	n/a
22	chr17:60005984-60006034	NHBE	bronchial:	n/a
23	chr17:60005984-60006034	LNCaP	prostate:	n/a
24	chr17:60005984-60006034	ECC-1	luminal epithelium:	n/a
25	chr17:60005984-60006034	MCF-7	breast:	n/a
26	chr17:60005984-60006034	ovcar-3	ovarian:	n/a
27	chr17:60005984-60006034	U87	brain:	n/a
28	chr17:60005984-60006034	A549	lung:	n/a
29	chr17:60005984-60006034	AG04450	lung:	fetal
30	chr17:60005984-60006034	AG09319	gingival:	n/a
31	chr17:60005984-60006034	GM06990	blood:	n/a
32	chr17:60005984-60006034	HPAEpiC	pulmonary alveolar:	n/a
33	chr17:60005984-60006034	HIPEpiC	eye:	n/a
34	chr17:60005984-60006034	BJ	skin:	n/a
35	chr17:60005984-60006034	HNPCEpiC	eye:	n/a
36	chr17:60005984-60006034	ProgFib	skin:	n/a
37	chr17:60005984-60006034	K562	blood:	n/a
38	chr17:60005984-60006034	CMK	blood:	n/a
39	chr17:60005984-60006034	BE2_C	brain:	n/a
40	chr17:60005984-60006034	Jurkat	blood:	n/a
41	chr17:60005984-60006034	GM12878	blood:	n/a
42	chr17:60005984-60006034	Hepatocyte	liver:	n/a
43	chr17:60005984-60006034	HEEpiC	esophagus:	n/a
44	chr17:60005984-60006034	GM12891	blood:	n/a
45	chr17:60005984-60006034	SK-N-MC	brain:	n/a
46	chr17:60005984-60006034	MCF10A-Er-Src	breast:	n/a
47	chr17:60005984-60006034	PrEC	prostate:	n/a
48	chr17:60005984-60006034	HCM	heart:	n/a
49	chr17:60005984-60006034	AG04449	skin:	fetal
50	chr17:60005984-60006034	SKMC	muscle:	n/a

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:60003720..60006070-chr17:60032703..60035089,4	MCF-7	breast:
2	chr17:59487584..59490320-chr17:60003961..60006356,2	MCF-7	breast:
3	chr17:59967952..59972166-chr17:60003800..60006338,4	MCF-7	breast:
4	chr17:60004037..60006603-chr7:148892637..148894393,2	MCF-7	breast:
5	chr17:59939694..59942407-chr17:60003159..60006084,4	K562	blood:
6	chr17:60003458..60007739-chr17:60031552..60035376,4	MCF-7	breast:
7	chr17:60005709..60008113-chr17:60023114..60025647,2	MCF-7	breast:
8	chr17:59959753..59962989-chr17:60003686..60006854,4	MCF-7	breast:
9	chr17:60004211..60007034-chr17:60081016..60083481,3	MCF-7	breast:
10	chr17:59939106..59942463-chr17:60003505..60006582,4	MCF-7	breast:
11	chr17:60003486..60006277-chr17:60141285..60143515,2	K562	blood:
12	chr17:60005081..60007593-chr3:197685672..197687423,2	MCF-7	breast:
13	chr17:59939071..59942892-chr17:60002944..60006795,10	MCF-7	breast:
14	chr17:60004432..60006975-chrX:153598237..153599773,2	MCF-7	breast:
15	chr17:59939694..59942713-chr17:60003159..60007024,4	K562	blood:
16	chr17:60002473..60006196-chr17:60142332..60145548,5	MCF-7	breast:
17	chr17:60003987..60006563-chr6:30582839..30584974,2	MCF-7	breast:
18	chr16:70412278..70414486-chr17:60004606..60007094,2	MCF-7	breast:
19	chr17:59951279..59952912-chr17:60004615..60006533,2	MCF-7	breast:
20	chr17:60004093..60006287-chr20:45946322..45948164,2	MCF-7	breast:
21	chr17:60002671..60006640-chr17:60140695..60145461,16	MCF-7	breast:

No data

Variant related genes	Relation type
INTS2	TF binding region
INTS2	CpG island
ENSG00000267882	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000260111	Chromatin interaction
ENSG00000185621	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000108506	Chromatin interaction
ENSG00000108510	Chromatin interaction
ENSG00000114473	Chromatin interaction
ENSG00000202361	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000170265	Chromatin interaction
ENSG00000242398	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000196924	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10401014	1.00[EUR][1000 genomes]
rs16945750	1.00[EUR][1000 genomes]
rs28431006	1.00[EUR][1000 genomes]
rs4988342	1.00[EUR][1000 genomes]
rs58046635	1.00[EUR][1000 genomes]
rs59794823	1.00[EUR][1000 genomes]
rs6504075	1.00[EUR][1000 genomes]
rs6504076	1.00[EUR][1000 genomes]
rs6504078	1.00[EUR][1000 genomes]
rs7211128	1.00[EUR][1000 genomes]
rs7212399	1.00[EUR][1000 genomes]
rs7212824	1.00[EUR][1000 genomes]
rs7212884	1.00[EUR][1000 genomes]
rs7213026	1.00[EUR][1000 genomes]
rs7217530	1.00[EUR][1000 genomes]
rs7221827	1.00[EUR][1000 genomes]
rs7222876	1.00[EUR][1000 genomes]
rs7224112	1.00[EUR][1000 genomes]
rs7226248	1.00[EUR][1000 genomes]
rs73991952	1.00[EUR][1000 genomes]
rs8065060	1.00[EUR][1000 genomes]
rs8068267	1.00[EUR][1000 genomes]
rs8069386	1.00[EUR][1000 genomes]
rs8069903	1.00[EUR][1000 genomes]
rs8069946	1.00[EUR][1000 genomes]
rs8078342	1.00[EUR][1000 genomes]
rs9783841	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9892063	1.00[EUR][1000 genomes]
rs9892123	1.00[EUR][1000 genomes]
rs9894718	1.00[EUR][1000 genomes]
rs9896768	1.00[EUR][1000 genomes]
rs9899042	1.00[EUR][1000 genomes]
rs9899780	1.00[EUR][1000 genomes]
rs9902699	1.00[EUR][1000 genomes]
rs9903562	1.00[EUR][1000 genomes]
rs9905888	1.00[EUR][1000 genomes]
rs9909145	1.00[EUR][1000 genomes]
rs9909882	1.00[EUR][1000 genomes]
rs9910067	1.00[EUR][1000 genomes]
rs9910252	1.00[EUR][1000 genomes]
rs9910902	1.00[EUR][1000 genomes]
rs9914007	1.00[EUR][1000 genomes]
rs9914605	1.00[EUR][1000 genomes]
rs9915023	1.00[EUR][1000 genomes]
rs9944467	1.00[EUR][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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60004200-60006200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr17:60005400-60018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr17:60005800-60006200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:60005800-60006200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr17:60005800-60017600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr17:60005800-60017800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr17:60005800-60017800	Weak transcription	Primary T cells from cord blood	blood
8	chr17:60005800-60017800	Weak transcription	Adipose Nuclei	Adipose
9	chr17:60005800-60022000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr17:60005800-60022000	Weak transcription	Thymus	Thymus
11	chr17:60005800-60022800	Weak transcription	Brain Angular Gyrus	brain
12	chr17:60006000-60006200	Enhancers	Dnd41	blood
13	chr17:60006000-60008200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:60006000-60017600	Weak transcription	A549	lung
15	chr17:60006000-60017600	Weak transcription	NH-A	brain
16	chr17:60006000-60017800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:60006000-60017800	Weak transcription	HSMM	muscle
18	chr17:60006000-60018000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr17:60006000-60018000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr17:60006000-60018400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:60006000-60018600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr17:60006000-60018600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr17:60006000-60019400	Weak transcription	Hela-S3	cervix
24	chr17:60006000-60019600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr17:60006000-60020400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr17:60006000-60020800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr17:60006000-60021000	Weak transcription	HMEC	breast
28	chr17:60006000-60021200	Weak transcription	Osteobl	bone
29	chr17:60006000-60021400	Weak transcription	HUVEC	blood vessel
30	chr17:60006000-60022000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr17:60006000-60022000	Weak transcription	Fetal Brain Female	brain
32	chr17:60006000-60022000	Weak transcription	HSMMtube	muscle
33	chr17:60006000-60022800	Weak transcription	Brain Anterior Caudate	brain
34	chr17:60006000-60023000	Weak transcription	Brain Hippocampus Middle	brain
35	chr17:60006000-60023600	Weak transcription	Stomach Smooth Muscle	stomach

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