Variant report

Variant	rs917533
Chromosome Location	chr17:59471082-59471083
allele	C/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:24)
LncRNA
region (count:12)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59469164..59471645-chr17:59472250..59474321,2	K562	blood:
2	chr17:59434168..59434686-chr17:59470583..59471420,2	MCF-7	breast:
3	chr17:59470667..59471725-chr17:59488553..59489465,8	MCF-7	breast:
4	chr17:59426772..59427336-chr17:59470592..59471244,2	MCF-7	breast:
5	chr17:59470571..59471324-chr17:59494235..59494804,2	MCF-7	breast:
6	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
7	chr17:59468937..59480240-chr20:49340039..49356868,49	MCF-7	breast:
8	chr17:59470884..59471787-chr20:49411053..49411955,4	MCF-7	breast:
9	chr17:59468469..59482635-chr20:45977748..45992950,51	MCF-7	breast:
10	chr17:56736472..56738107-chr17:59470143..59472768,3	MCF-7	breast:
11	chr17:59470745..59471404-chr17:59628558..59629186,2	MCF-7	breast:
12	chr17:59079334..59080155-chr17:59470561..59471226,2	MCF-7	breast:
13	chr11:63951691..63953580-chr17:59469682..59471270,2	MCF-7	breast:
14	chr17:59470592..59472862-chr9:115912081..115913641,2	MCF-7	breast:
15	chr17:58797933..58798712-chr17:59470658..59471353,2	MCF-7	breast:
16	chr17:59470525..59474011-chr17:59486288..59490375,89	MCF-7	breast:
17	chr17:59470522..59472690-chr20:55839093..55841752,2	MCF-7	breast:
18	chr17:59468167..59483990-chr20:49341590..49352501,35	MCF-7	breast:
19	chr17:59470609..59471850-chr20:49410193..49412110,32	MCF-7	breast:
20	chr17:59469231..59471206-chr20:45988414..45990952,2	MCF-7	breast:
21	chr17:59435176..59436050-chr17:59470693..59471414,2	MCF-7	breast:
22	chr17:59470233..59471237-chr20:52195063..52195793,3	MCF-7	breast:
23	chr17:59447417..59500105-chr20:49391742..49424382,639	MCF-7	breast:
24	chr11:18654582..18656464-chr17:59469596..59471127,2	MCF-7	breast:

(count:12 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NACA2-2	chr17:59470838-59471108	XLOC_012542
2	lnc-NACA2-2	chr17:59470821-59471108	XLOC_012542
3	lnc-NACA2-2	chr17:59470827-59471108	XLOC_012542
4	lnc-NACA2-2	chr17:59470819-59471108	ENSG00000267280.1
5	lnc-NACA2-2	chr17:59470819-59471108	ENSG00000267280.1
6	lnc-NACA2-2	chr17:59470827-59471108	NONHSAT055129
7	lnc-NACA2-2	chr17:59470242-59472935	ucscGeneNc_uc002jdy_1
8	lnc-NACA2-2	chr17:59470818-59471108	ENSG00000267280.1
9	lnc-NACA2-2	chr17:59470819-59471108	ENSG00000267280.1
10	lnc-NACA2-2	chr17:59470817-59471108	ENSG00000267280.1
11	lnc-NACA2-2	chr17:59470819-59471108	ENSG00000267280.1
12	lnc-NACA2-2	chr17:59470828-59471108	NONHSAT055130

No data

Variant related genes	Relation type
ENSG00000124171	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000141376	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000168439	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000124243	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000136867	Chromatin interaction
ENSG00000179119	Chromatin interaction
ENSG00000273451	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11656616	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[ASN][1000 genomes]
rs2109019	0.85[ASW][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap]
rs9907379	0.85[ASW][hapmap];0.81[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	nsv908665	chr17:59470193-59494574	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
9	nsv908666	chr17:59470842-59489822	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	253 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs917533	NACA2	cis	cerebellum	SCAN
rs917533	DYNLL2	cis	parietal	SCAN
rs917533	PTRH2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59444600-59473400	Weak transcription	Right Atrium	heart
2	chr17:59447000-59473400	Weak transcription	Pancreas	Pancrea
3	chr17:59462400-59471600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr17:59464000-59474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr17:59467400-59471800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr17:59467400-59474000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr17:59467600-59471200	Weak transcription	Brain Substantia Nigra	brain
8	chr17:59467600-59471400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr17:59467600-59472800	Weak transcription	Adipose Nuclei	Adipose
10	chr17:59467800-59471200	Weak transcription	NHDF-Ad	bronchial
11	chr17:59467800-59472800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr17:59467800-59473800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:59468000-59472200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr17:59468400-59471600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr17:59470000-59471200	Enhancers	HepG2	liver
16	chr17:59470000-59471800	Weak transcription	Right Ventricle	heart
17	chr17:59470600-59472000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr17:59470600-59472200	Enhancers	Fetal Lung	lung
19	chr17:59470600-59472400	Weak transcription	Spleen	Spleen
20	chr17:59470600-59472800	Enhancers	Hela-S3	cervix
21	chr17:59470600-59473600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:59470800-59471200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr17:59470800-59471600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr17:59470800-59471600	Enhancers	Esophagus	oesophagus
25	chr17:59470800-59471600	Genic enhancers	NHLF	lung
26	chr17:59470800-59472000	Enhancers	HSMMtube	muscle
27	chr17:59470800-59472200	Enhancers	Osteobl	bone
28	chr17:59470800-59472400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:59470800-59472400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr17:59470800-59472800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr17:59470800-59473200	Enhancers	Placenta	Placenta
32	chr17:59470800-59476000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr17:59471000-59471200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
34	chr17:59471000-59471200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr17:59471000-59471200	Enhancers	Psoas Muscle	Psoas
36	chr17:59471000-59471400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr17:59471000-59471400	Weak transcription	Brain Hippocampus Middle	brain
38	chr17:59471000-59471400	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr17:59471000-59471600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
40	chr17:59471000-59471600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr17:59471000-59471800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:59471000-59471800	Enhancers	Fetal Heart	heart
43	chr17:59471000-59471800	Enhancers	Lung	lung
44	chr17:59471000-59471800	Enhancers	Ovary	ovary
45	chr17:59471000-59471800	Enhancers	A549	lung
46	chr17:59471000-59472200	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr17:59471000-59472200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr17:59471000-59472200	Enhancers	Gastric	stomach
49	chr17:59471000-59472800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
50	chr17:59471000-59473200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links