Variant report

Variant	rs3785839
Chromosome Location	chr17:59456420-59456421
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr17:59456184-59456725	HepG2	liver:	n/a	n/a
2	FOXA1	chr17:59456192-59456716	HepG2	liver:	n/a	n/a
3	HNF4A	chr17:59456217-59456758	HepG2	liver:	n/a	n/a
4	EP300	chr17:59456018-59456778	HepG2	liver:	n/a	chr17:59456402-59456411 chr17:59456333-59456342
5	TEAD4	chr17:59456108-59458164	A549	lung:	n/a	n/a
6	FOXA1	chr17:59456206-59456786	HepG2	liver:	n/a	n/a
7	RXRA	chr17:59456221-59456740	HepG2	liver:	n/a	chr17:59456284-59456304
8	HDAC2	chr17:59456161-59456751	HepG2	liver:	n/a	n/a
9	MYBL2	chr17:59456178-59456943	HepG2	liver:	n/a	n/a
10	PML	chr17:59453151-59459663	MCF-7	breast:	n/a	chr17:59457571-59457579 chr17:59454056-59454064
11	POLR2A	chr17:59456015-59456902	ProgFib	skin:	n/a	n/a
12	SP1	chr17:59456143-59456735	HepG2	liver:	n/a	n/a
13	ZBTB7A	chr17:59456150-59456591	HepG2	liver:	n/a	n/a
14	FOXA1	chr17:59456291-59456704	HepG2	liver:	n/a	n/a
15	NFIC	chr17:59456283-59456754	HepG2	liver:	n/a	n/a
16	ZBTB7A	chr17:59456291-59456584	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
2	chr17:59455619..59457341-chr17:59935158..59937112,2	MCF-7	breast:
3	chr17:59456299..59459138-chr20:45979827..45981645,2	MCF-7	breast:
4	chr17:59455431..59456976-chr19:462107..463610,2	MCF-7	breast:
5	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
ENSG00000124243	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000101040	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1004492	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10853030	0.81[ASN][1000 genomes]
rs11079427	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12451110	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2286530	0.88[CHB][hapmap]
rs4968557	0.85[CEU][hapmap]
rs4968558	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs7214149	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7219624	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs8072961	0.85[CEU][hapmap]
rs8080537	0.85[CEU][hapmap]
rs929471	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs9891004	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[YRI][hapmap];0.88[EUR][1000 genomes]
rs9899196	0.87[ASN][1000 genomes]
rs9907356	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs9914215	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:47 , 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	chr17:59444000-59457400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr17:59444200-59460400	Weak transcription	Left Ventricle	heart
6	chr17:59444400-59467000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr17:59444600-59456600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr17:59444600-59458400	Weak transcription	Brain Anterior Caudate	brain
9	chr17:59444600-59459800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr17:59444600-59460600	Weak transcription	Right Ventricle	heart
11	chr17:59444600-59473400	Weak transcription	Right Atrium	heart
12	chr17:59445000-59462200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr17:59446800-59464600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr17:59447000-59458000	Weak transcription	Brain Hippocampus Middle	brain
15	chr17:59447000-59458400	Weak transcription	Brain Angular Gyrus	brain
16	chr17:59447000-59458600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr17:59447000-59473400	Weak transcription	Pancreas	Pancrea
18	chr17:59447200-59458000	Weak transcription	Brain Substantia Nigra	brain
19	chr17:59447200-59458400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:59447200-59467000	Weak transcription	Gastric	stomach
21	chr17:59447400-59466800	Weak transcription	Fetal Intestine Small	intestine
22	chr17:59448600-59458000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr17:59451600-59467000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr17:59453000-59457400	Weak transcription	Fetal Lung	lung
25	chr17:59453400-59459600	Enhancers	Fetal Muscle Leg	muscle
26	chr17:59454000-59456800	Enhancers	Psoas Muscle	Psoas
27	chr17:59454400-59458000	Enhancers	Fetal Muscle Trunk	muscle
28	chr17:59454600-59462600	Enhancers	NHDF-Ad	bronchial
29	chr17:59454800-59456800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:59454800-59458200	Enhancers	Adipose Nuclei	Adipose
31	chr17:59455200-59463400	Weak transcription	HSMMtube	muscle
32	chr17:59455400-59457400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr17:59455600-59457000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr17:59455600-59457400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:59455600-59458600	Enhancers	Fetal Kidney	kidney
36	chr17:59455600-59466800	Weak transcription	Lung	lung
37	chr17:59455800-59456800	Strong transcription	Primary T cells from cord blood	blood
38	chr17:59455800-59457800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr17:59456000-59456600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr17:59456200-59456600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr17:59456200-59456800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr17:59456200-59457200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr17:59456200-59457400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr17:59456200-59467000	Weak transcription	Aorta	Aorta
45	chr17:59456400-59457200	Enhancers	Spleen	Spleen
46	chr17:59456400-59457200	Flanking Active TSS	HepG2	liver
47	chr17:59456400-59457200	Enhancers	NHLF	lung

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