Variant report

Variant	rs2286530
Chromosome Location	chr17:59470055-59470056
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59469164..59471645-chr17:59472250..59474321,2	K562	blood:
2	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
3	chr17:59468937..59480240-chr20:49340039..49356868,49	MCF-7	breast:
4	chr17:59468469..59482635-chr20:45977748..45992950,51	MCF-7	breast:
5	chr17:59468443..59470783-chr3:63106998..63109509,2	MCF-7	breast:
6	chr11:63951691..63953580-chr17:59469682..59471270,2	MCF-7	breast:
7	chr17:59468167..59483990-chr20:49341590..49352501,35	MCF-7	breast:
8	chr17:59467424..59470121-chr20:49376913..49378650,2	MCF-7	breast:
9	chr17:59469231..59471206-chr20:45988414..45990952,2	MCF-7	breast:
10	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:
11	chr11:18654582..18656464-chr17:59469596..59471127,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168439	Chromatin interaction
ENSG00000273451	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000179119	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000124243	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1004492	0.81[ASN][1000 genomes]
rs10853030	0.83[ASN][1000 genomes]
rs3785839	0.88[CHB][hapmap]
rs4968558	0.83[ASN][1000 genomes]
rs7214149	0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs9891004	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv908663	chr17:59464069-59521310	Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	278 gene(s)	inside rSNPs	diseases
7	nsv908664	chr17:59465697-59491030	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2286530	TUBD1	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59438200-59470800	Weak transcription	Esophagus	oesophagus
2	chr17:59444600-59473400	Weak transcription	Right Atrium	heart
3	chr17:59447000-59473400	Weak transcription	Pancreas	Pancrea
4	chr17:59462400-59471600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr17:59462600-59470800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:59464000-59471000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr17:59464000-59474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr17:59467400-59470600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr17:59467400-59470800	Weak transcription	Brain Anterior Caudate	brain
10	chr17:59467400-59470800	Weak transcription	Osteobl	bone
11	chr17:59467400-59471800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr17:59467400-59474000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:59467600-59471000	Weak transcription	Ovary	ovary
14	chr17:59467600-59471200	Weak transcription	Brain Substantia Nigra	brain
15	chr17:59467600-59471400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr17:59467600-59472800	Weak transcription	Adipose Nuclei	Adipose
17	chr17:59467800-59471000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr17:59467800-59471000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr17:59467800-59471000	Weak transcription	A549	lung
20	chr17:59467800-59471200	Weak transcription	NHDF-Ad	bronchial
21	chr17:59467800-59472800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr17:59467800-59473800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr17:59468000-59471000	Weak transcription	Fetal Heart	heart
24	chr17:59468000-59472200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:59468200-59471000	Weak transcription	Lung	lung
26	chr17:59468400-59471600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr17:59468600-59470200	Weak transcription	NHLF	lung
28	chr17:59469000-59470200	Strong transcription	Fetal Intestine Small	intestine
29	chr17:59469200-59470800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr17:59469400-59470200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr17:59469400-59470800	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr17:59469600-59470200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr17:59469600-59470200	Enhancers	Stomach Smooth Muscle	stomach
34	chr17:59469600-59470600	Strong transcription	Spleen	Spleen
35	chr17:59469600-59470800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr17:59469600-59471000	Weak transcription	Gastric	stomach
37	chr17:59469800-59470400	Strong transcription	Fetal Lung	lung
38	chr17:59469800-59471000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr17:59470000-59470400	Weak transcription	Brain Hippocampus Middle	brain
40	chr17:59470000-59471200	Enhancers	HepG2	liver
41	chr17:59470000-59471800	Weak transcription	Right Ventricle	heart

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