Variant report

Variant	rs6504040
Chromosome Location	chr17:59460854-59460855
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	GATA2	chr17:59460791-59462699	SH-SY5Y	brain:	n/a	chr17:59460990-59460999 chr17:59460990-59461000 chr17:59460989-59461001 chr17:59460992-59460999 chr17:59460992-59460999 chr17:59460987-59461003 chr17:59460987-59461003 chr17:59460992-59460999 chr17:59460985-59461006
2	EP300	chr17:59459910-59464367	SK-N-SH	brain:	n/a	chr17:59463203-59463217 chr17:59461941-59461954
3	POLR2A	chr17:59460284-59461128	ProgFib	skin:	n/a	n/a
4	RAD21	chr17:59460705-59461448	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr17:59460826-59461470	SK-N-SH_RA	brain:	n/a	n/a
6	GATA3	chr17:59460839-59461369	SK-N-SH	brain:	n/a	chr17:59460990-59460999 chr17:59460990-59461000 chr17:59460989-59461001 chr17:59460992-59460999 chr17:59460992-59460999 chr17:59460987-59461003 chr17:59460987-59461003 chr17:59460992-59460999 chr17:59460985-59461006
7	YY1	chr17:59460829-59461311	SK-N-SH_RA	brain:	n/a	n/a
8	TEAD4	chr17:59460065-59460859	A549	lung:	n/a	n/a
9	TCF12	chr17:59460674-59461552	SK-N-SH	brain:	n/a	chr17:59461358-59461365

No.	Distal block	Cell Line	Cell type
1	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
2	chr17:59460298..59460944-chr20:49411016..49411865,2	MCF-7	breast:
3	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBX2-3	chr17:59460762-59460915	ENSG00000266934.1

Variant related genes	Relation type
BCAS3	TF binding region
ENSG00000124243	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16945213	1.00[EUR][1000 genomes]
rs57045595	1.00[EUR][1000 genomes]
rs58582622	1.00[EUR][1000 genomes]
rs60549606	1.00[EUR][1000 genomes]
rs6504041	1.00[EUR][1000 genomes]
rs7211905	1.00[EUR][1000 genomes]
rs7214625	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7219765	1.00[EUR][1000 genomes]
rs73322588	1.00[EUR][1000 genomes]
rs73991905	1.00[EUR][1000 genomes]
rs73991907	1.00[EUR][1000 genomes]
rs73991919	1.00[EUR][1000 genomes]
rs9891905	1.00[EUR][1000 genomes]
rs9911414	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv1796927	chr17:59460119-59495319	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	270 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 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	chr17:59444400-59467000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr17:59444600-59473400	Weak transcription	Right Atrium	heart
6	chr17:59445000-59462200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr17:59446800-59464600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:59447000-59473400	Weak transcription	Pancreas	Pancrea
9	chr17:59447200-59467000	Weak transcription	Gastric	stomach
10	chr17:59447400-59466800	Weak transcription	Fetal Intestine Small	intestine
11	chr17:59451600-59467000	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr17:59454600-59462600	Enhancers	NHDF-Ad	bronchial
13	chr17:59455200-59463400	Weak transcription	HSMMtube	muscle
14	chr17:59455600-59466800	Weak transcription	Lung	lung
15	chr17:59456200-59467000	Weak transcription	Aorta	Aorta
16	chr17:59456600-59461800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr17:59456800-59464800	Weak transcription	Primary T cells from cord blood	blood
18	chr17:59457000-59461400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr17:59457200-59461200	Weak transcription	Spleen	Spleen
20	chr17:59457800-59461000	Enhancers	HepG2	liver
21	chr17:59457800-59463000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:59458000-59467000	Weak transcription	Osteobl	bone
23	chr17:59458200-59461600	Weak transcription	Placenta	Placenta
24	chr17:59458600-59467200	Weak transcription	Fetal Kidney	kidney
25	chr17:59458800-59466600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr17:59459000-59461400	Enhancers	Fetal Muscle Trunk	muscle
27	chr17:59459200-59461200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr17:59459200-59462000	Weak transcription	Fetal Brain Female	brain
29	chr17:59459200-59463200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:59459200-59466800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr17:59459200-59469400	Weak transcription	Brain Hippocampus Middle	brain
32	chr17:59459400-59463400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr17:59460000-59463800	Enhancers	Fetal Muscle Leg	muscle
34	chr17:59460000-59464000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr17:59460200-59461000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr17:59460200-59462400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr17:59460200-59464200	Enhancers	Fetal Lung	lung
38	chr17:59460400-59461000	Enhancers	Left Ventricle	heart
39	chr17:59460400-59462400	Enhancers	Adipose Nuclei	Adipose
40	chr17:59460400-59463200	Bivalent Enhancer	Fetal Stomach	stomach
41	chr17:59460400-59464200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr17:59460600-59461600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr17:59460600-59461800	Genic enhancers	NHLF	lung
44	chr17:59460600-59462200	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr17:59460800-59461400	Weak transcription	Right Ventricle	heart
46	chr17:59460800-59462600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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