Variant report

Variant	rs1004492
Chromosome Location	chr17:59457203-59457204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr17:59457041-59458165	MCF-7	breast:	n/a	n/a
2	RCOR1	chr17:59457176-59457667	HepG2	liver:	n/a	n/a
3	TEAD4	chr17:59456108-59458164	A549	lung:	n/a	n/a
4	PML	chr17:59453151-59459663	MCF-7	breast:	n/a	chr17:59457571-59457579 chr17:59454056-59454064
5	MXI1	chr17:59456952-59459518	SK-N-SH	brain:	n/a	n/a
6	EP300	chr17:59457125-59459625	SK-N-SH	brain:	n/a	chr17:59457598-59457614 chr17:59458171-59458185

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	chr17:59455619..59457341-chr17:59935158..59937112,2	MCF-7	breast:
4	chr17:59456299..59459138-chr20:45979827..45981645,2	MCF-7	breast:
5	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

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

Variant related genes	Relation type
ENSG00000266934	TF binding region
ENSG00000124243	Chromatin interaction
ENSG00000160179	Chromatin interaction
ENSG00000231119	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]
rs10853030	0.97[ASN][1000 genomes]
rs11079427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12451110	0.85[EUR][1000 genomes]
rs2286530	0.81[ASN][1000 genomes]
rs3785839	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4968557	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs4968558	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs7214149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7219624	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs8072961	1.00[CEU][hapmap]
rs8080537	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs929471	1.00[CEU][hapmap]
rs9889520	0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs9891004	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9899196	0.80[AMR][1000 genomes]
rs9907356	1.00[CEU][hapmap]

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	chr17:59444000-59457400	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	chr17:59444600-59458400	Weak transcription	Brain Anterior Caudate	brain
8	chr17:59444600-59459800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr17:59444600-59460600	Weak transcription	Right Ventricle	heart
10	chr17:59444600-59473400	Weak transcription	Right Atrium	heart
11	chr17:59445000-59462200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:59446800-59464600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:59447000-59458000	Weak transcription	Brain Hippocampus Middle	brain
14	chr17:59447000-59458400	Weak transcription	Brain Angular Gyrus	brain
15	chr17:59447000-59458600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr17:59447000-59473400	Weak transcription	Pancreas	Pancrea
17	chr17:59447200-59458000	Weak transcription	Brain Substantia Nigra	brain
18	chr17:59447200-59458400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:59447200-59467000	Weak transcription	Gastric	stomach
20	chr17:59447400-59466800	Weak transcription	Fetal Intestine Small	intestine
21	chr17:59448600-59458000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr17:59451600-59467000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr17:59453000-59457400	Weak transcription	Fetal Lung	lung
24	chr17:59453400-59459600	Enhancers	Fetal Muscle Leg	muscle
25	chr17:59454400-59458000	Enhancers	Fetal Muscle Trunk	muscle
26	chr17:59454600-59462600	Enhancers	NHDF-Ad	bronchial
27	chr17:59454800-59458200	Enhancers	Adipose Nuclei	Adipose
28	chr17:59455200-59463400	Weak transcription	HSMMtube	muscle
29	chr17:59455400-59457400	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr17:59455600-59457400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr17:59455600-59458600	Enhancers	Fetal Kidney	kidney
32	chr17:59455600-59466800	Weak transcription	Lung	lung
33	chr17:59455800-59457800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr17:59456200-59457400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:59456200-59467000	Weak transcription	Aorta	Aorta
36	chr17:59456600-59458000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr17:59456600-59458600	Enhancers	Fetal Stomach	stomach
38	chr17:59456600-59461800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr17:59456800-59460200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr17:59456800-59464800	Weak transcription	Primary T cells from cord blood	blood
41	chr17:59457000-59457600	Bivalent Enhancer	Placenta	Placenta
42	chr17:59457000-59458600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr17:59457000-59461400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr17:59457200-59457600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr17:59457200-59457600	Enhancers	HepG2	liver
46	chr17:59457200-59458000	Flanking Active TSS	NHLF	lung
47	chr17:59457200-59458200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr17:59457200-59461200	Weak transcription	Spleen	Spleen

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