Variant report

Variant	rs16945232
Chromosome Location	chr17:59457431-59457432
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr17:59457415-59458039	HEK293-T-REx	kidney:	n/a	chr17:59457645-59457654 chr17:59457646-59457667
2	GATA3	chr17:59457041-59458165	MCF-7	breast:	n/a	n/a
3	HDAC2	chr17:59457253-59457698	HepG2	liver:	n/a	chr17:59457532-59457546
4	POLR2A	chr17:59457210-59457524	Hela-S3	cervix:	n/a	n/a
5	HNF4A	chr17:59457234-59457662	HepG2	liver:	n/a	chr17:59457493-59457508 chr17:59457440-59457455 chr17:59457494-59457508
6	RCOR1	chr17:59457176-59457667	HepG2	liver:	n/a	n/a
7	HNF4A	chr17:59457265-59457607	HepG2	liver:	n/a	chr17:59457493-59457508 chr17:59457440-59457455 chr17:59457494-59457508
8	RAD21	chr17:59457409-59458904	SK-N-SH_RA	brain:	n/a	chr17:59458049-59458059 chr17:59458317-59458331
9	TEAD4	chr17:59456108-59458164	A549	lung:	n/a	n/a
10	HNF4G	chr17:59457287-59457717	HepG2	liver:	n/a	chr17:59457493-59457508 chr17:59457494-59457508
11	POLR2A	chr17:59457244-59457829	ProgFib	skin:	n/a	n/a
12	PML	chr17:59453151-59459663	MCF-7	breast:	n/a	chr17:59457571-59457579 chr17:59454056-59454064
13	MXI1	chr17:59456952-59459518	SK-N-SH	brain:	n/a	n/a
14	ELF1	chr17:59457325-59457585	HepG2	liver:	n/a	n/a
15	EP300	chr17:59457125-59459625	SK-N-SH	brain:	n/a	chr17:59457598-59457614 chr17:59458171-59458185

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:59457396-59457446	HepG2	liver:	n/a
2	chr17:59457396-59457446	HCM	heart:	n/a
3	chr17:59457396-59457446	T-47D	breast:	n/a
4	chr17:59457396-59457446	PFSK-1	brain:	n/a
5	chr17:59457396-59457446	HAEpiC	amniotic membrane:	n/a
6	chr17:59457396-59457446	K562	blood:	n/a
7	chr17:59457396-59457446	AG10803	skin:	n/a
8	chr17:59457396-59457446	MCF10A-Er-Src	breast:	n/a
9	chr17:59457396-59457446	LNCaP	prostate:	n/a
10	chr17:59457396-59457446	HRPEpiC	eye:	n/a
11	chr17:59457396-59457446	SKMC	muscle:	n/a
12	chr17:59457396-59457446	HCF	heart:	n/a
13	chr17:59457396-59457446	Hepatocyte	liver:	n/a
14	chr17:59457396-59457446	PANC-1	pancreas:	n/a
15	chr17:59457396-59457446	H1-hESC	embryonic stem cell:	embryo
16	chr17:59457396-59457446	AG04450	lung:	fetal
17	chr17:59457396-59457446	U87	brain:	n/a
18	chr17:59457396-59457446	Hela-S3	cervix:	n/a
19	chr17:59457396-59457446	SK-N-SH	brain:	n/a
20	chr17:59457396-59457446	SAEC	small airway:	n/a
21	chr17:59457396-59457446	NHBE	bronchial:	n/a
22	chr17:59457396-59457446	AG04449	skin:	fetal
23	chr17:59457396-59457446	HUVEC	blood vessel:	n/a
24	chr17:59457396-59457446	RPTEC	kidney:	n/a
25	chr17:59457396-59457446	HPAEpiC	pulmonary alveolar:	n/a
26	chr17:59457396-59457446	ECC-1	luminal epithelium:	n/a
27	chr17:59457396-59457446	PrEC	prostate:	n/a
28	chr17:59457396-59457446	HL-60	blood:	n/a
29	chr17:59457396-59457446	GM12891	blood:	n/a
30	chr17:59457396-59457446	ProgFib	skin:	n/a
31	chr17:59457396-59457446	AG09319	gingival:	n/a
32	chr17:59457396-59457446	A549	lung:	n/a
33	chr17:59457396-59457446	HRCEpiC	kidney:	n/a
34	chr17:59457396-59457446	HMEC	breast:	n/a
35	chr17:59457396-59457446	HCT-116	colon:	n/a
36	chr17:59457396-59457446	SK-N-SH_RA	brain:	n/a
37	chr17:59457396-59457446	GM12878	blood:	n/a
38	chr17:59457396-59457446	NT2-D1	testis:	n/a
39	chr17:59457396-59457446	Jurkat	blood:	n/a
40	chr17:59457396-59457446	HRE	kidney:	n/a
41	chr17:59457396-59457446	HEEpiC	esophagus:	n/a
42	chr17:59457396-59457446	BE2_C	brain:	n/a
43	chr17:59457396-59457446	NH-A	brain:	n/a
44	chr17:59457396-59457446	AG09309	skin:	n/a
45	chr17:59457396-59457446	SK-N-MC	brain:	n/a
46	chr17:59457396-59457446	HNPCEpiC	eye:	n/a
47	chr17:59457396-59457446	HEK293	kidney:	embryo
48	chr17:59457396-59457446	ovcar-3	ovarian:	n/a
49	chr17:59457396-59457446	MCF-7	breast:	n/a
50	chr17:59457396-59457446	GM12892	blood:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
2	chr17:59456486..59458237-chr21:43674263..43677018,2	MCF-7	breast:
3	chr17:59456299..59459138-chr20:45979827..45981645,2	MCF-7	breast:
4	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBX2-4	chr17:59455191-59457933	NONHSAT055118

No data

Variant related genes	Relation type
ENSG00000266934	TF binding region
ENSG00000266934	CpG island
ENSG00000231119	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000160179	Chromatin interaction
ENSG00000101040	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1010270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10515196	1.00[JPT][hapmap]
rs16945174	1.00[JPT][hapmap]
rs16945233	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3785838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4459608	1.00[JPT][hapmap]
rs61037824	0.93[ASN][1000 genomes]
rs7211156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7215875	0.89[ASN][1000 genomes]
rs734375	1.00[JPT][hapmap]
rs73991903	0.89[ASN][1000 genomes]
rs73991905	0.89[ASN][1000 genomes]
rs73991906	0.89[ASN][1000 genomes]
rs73993479	0.93[ASN][1000 genomes]
rs758600	1.00[JPT][hapmap]
rs8066259	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	nsv518130	chr17:59456589-59491281	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	265 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59438200-59470800	Weak transcription	Esophagus	oesophagus
2	chr17:59440200-59462800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:59441600-59462200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:59444200-59460400	Weak transcription	Left Ventricle	heart
5	chr17:59444400-59467000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:59444600-59458400	Weak transcription	Brain Anterior Caudate	brain
7	chr17:59444600-59459800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr17:59444600-59460600	Weak transcription	Right Ventricle	heart
9	chr17:59444600-59473400	Weak transcription	Right Atrium	heart
10	chr17:59445000-59462200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr17:59446800-59464600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:59447000-59458000	Weak transcription	Brain Hippocampus Middle	brain
13	chr17:59447000-59458400	Weak transcription	Brain Angular Gyrus	brain
14	chr17:59447000-59458600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr17:59447000-59473400	Weak transcription	Pancreas	Pancrea
16	chr17:59447200-59458000	Weak transcription	Brain Substantia Nigra	brain
17	chr17:59447200-59458400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr17:59447200-59467000	Weak transcription	Gastric	stomach
19	chr17:59447400-59466800	Weak transcription	Fetal Intestine Small	intestine
20	chr17:59448600-59458000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr17:59451600-59467000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr17:59453400-59459600	Enhancers	Fetal Muscle Leg	muscle
23	chr17:59454400-59458000	Enhancers	Fetal Muscle Trunk	muscle
24	chr17:59454600-59462600	Enhancers	NHDF-Ad	bronchial
25	chr17:59454800-59458200	Enhancers	Adipose Nuclei	Adipose
26	chr17:59455200-59463400	Weak transcription	HSMMtube	muscle
27	chr17:59455600-59458600	Enhancers	Fetal Kidney	kidney
28	chr17:59455600-59466800	Weak transcription	Lung	lung
29	chr17:59455800-59457800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:59456200-59467000	Weak transcription	Aorta	Aorta
31	chr17:59456600-59458000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr17:59456600-59458600	Enhancers	Fetal Stomach	stomach
33	chr17:59456600-59461800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr17:59456800-59460200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:59456800-59464800	Weak transcription	Primary T cells from cord blood	blood
36	chr17:59457000-59457600	Bivalent Enhancer	Placenta	Placenta
37	chr17:59457000-59458600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr17:59457000-59461400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr17:59457200-59457600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr17:59457200-59457600	Enhancers	HepG2	liver
41	chr17:59457200-59458000	Flanking Active TSS	NHLF	lung
42	chr17:59457200-59458200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr17:59457200-59461200	Weak transcription	Spleen	Spleen
44	chr17:59457400-59458000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr17:59457400-59459200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:59457400-59459200	Enhancers	Fetal Lung	lung
47	chr17:59457400-59460400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr17:59457400-59460600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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