Variant report

Variant	rs10853030
Chromosome Location	chr17:59463239-59463240
allele	A/G
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	EP300	chr17:59463163-59463589	SK-N-SH_RA	brain:	n/a	chr17:59463203-59463217
2	FOS	chr17:59463212-59463582	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr17:59463233-59463579	IMR90	lung:	n/a	n/a
4	RAD21	chr17:59463091-59463557	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr17:59463200-59463350	BE2_C	brain:	n/a	chr17:59463333-59463341
6	EP300	chr17:59463179-59463623	SK-N-SH_RA	brain:	n/a	chr17:59463203-59463217
7	CTCF	chr17:59463220-59463370	HPAF	blood vessel:	n/a	chr17:59463333-59463341
8	RAD21	chr17:59463188-59463456	HepG2	liver:	n/a	n/a
9	EP300	chr17:59459910-59464367	SK-N-SH	brain:	n/a	chr17:59463203-59463217 chr17:59461941-59461954
10	SMC3	chr17:59463156-59463396	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr17:59463120-59463270	BE2_C	brain:	n/a	n/a
12	CTCF	chr17:59463220-59463370	WERI-Rb-1	eye:	n/a	chr17:59463333-59463341
13	CTCF	chr17:59463205-59463472	IMR90	lung:	n/a	chr17:59463333-59463341
14	CTCF	chr17:59463220-59463370	HPF	lung:	n/a	chr17:59463333-59463341
15	RCOR1	chr17:59463071-59463688	IMR90	lung:	n/a	n/a
16	CTCF	chr17:59463200-59463350	RPTEC	kidney:	n/a	chr17:59463333-59463341
17	RAD21	chr17:59463175-59463491	HepG2	liver:	n/a	n/a
18	RAD21	chr17:59463152-59463477	SK-N-SH_RA	brain:	n/a	n/a
19	CTCF	chr17:59463200-59463350	AG09309	skin:	n/a	chr17:59463333-59463341
20	CTCF	chr17:59463140-59463290	HA-sp	spinal cord:	n/a	n/a
21	CTCF	chr17:59463234-59463408	HepG2	liver:	n/a	chr17:59463333-59463341
22	RAD21	chr17:59463190-59463454	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:234746035..234748207-chr17:59462933..59465026,2	MCF-7	breast:
2	chr17:59307160..59308095-chr17:59462995..59463857,2	MCF-7	breast:
3	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
4	chr17:59462327..59463954-chr20:49410845..49411916,17	MCF-7	breast:
5	chr17:59431974..59432671-chr17:59463189..59463785,2	MCF-7	breast:
6	chr17:59462853..59463565-chr20:49411331..49412286,3	MCF-7	breast:
7	chr17:59069140..59070696-chr17:59462060..59464804,2	K562	blood:
8	chr17:59461121..59463761-chr9:140044339..140046291,2	MCF-7	breast:
9	chr17:59462854..59463760-chr20:49409716..49410492,2	MCF-7	breast:
10	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:

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

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1004492	0.97[ASN][1000 genomes]
rs11079427	0.95[ASN][1000 genomes]
rs2286530	0.83[ASN][1000 genomes]
rs3785839	0.81[ASN][1000 genomes]
rs4968557	0.83[ASN][1000 genomes]
rs4968558	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214149	0.97[ASN][1000 genomes]
rs9889520	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9891004	0.97[ASN][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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59438200-59470800	Weak transcription	Esophagus	oesophagus
2	chr17:59444400-59467000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr17:59444600-59473400	Weak transcription	Right Atrium	heart
4	chr17:59446800-59464600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr17:59447000-59473400	Weak transcription	Pancreas	Pancrea
6	chr17:59447200-59467000	Weak transcription	Gastric	stomach
7	chr17:59447400-59466800	Weak transcription	Fetal Intestine Small	intestine
8	chr17:59451600-59467000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr17:59455200-59463400	Weak transcription	HSMMtube	muscle
10	chr17:59455600-59466800	Weak transcription	Lung	lung
11	chr17:59456200-59467000	Weak transcription	Aorta	Aorta
12	chr17:59456800-59464800	Weak transcription	Primary T cells from cord blood	blood
13	chr17:59458000-59467000	Weak transcription	Osteobl	bone
14	chr17:59458600-59467200	Weak transcription	Fetal Kidney	kidney
15	chr17:59458800-59466600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr17:59459200-59466800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr17:59459200-59469400	Weak transcription	Brain Hippocampus Middle	brain
18	chr17:59459400-59463400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr17:59460000-59463800	Enhancers	Fetal Muscle Leg	muscle
20	chr17:59460000-59464000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:59460200-59464200	Enhancers	Fetal Lung	lung
22	chr17:59460400-59464200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:59461000-59467000	Weak transcription	Left Ventricle	heart
24	chr17:59461400-59466800	Weak transcription	Spleen	Spleen
25	chr17:59462000-59463400	Enhancers	Fetal Brain Female	brain
26	chr17:59462000-59466800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr17:59462000-59466800	Weak transcription	NHLF	lung
28	chr17:59462400-59463400	Weak transcription	Right Ventricle	heart
29	chr17:59462400-59466800	Weak transcription	Adipose Nuclei	Adipose
30	chr17:59462400-59471600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr17:59462600-59463800	Weak transcription	HepG2	liver
32	chr17:59462600-59464000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr17:59462600-59470800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr17:59462800-59463800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr17:59462800-59464000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr17:59462800-59464000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr17:59463000-59464000	Enhancers	NHDF-Ad	bronchial
38	chr17:59463000-59466800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr17:59463200-59463600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr17:59463200-59464000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr17:59463200-59464000	Enhancers	Fetal Stomach	stomach
42	chr17:59463200-59469400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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