Variant report

Variant	rs17301132
Chromosome Location	chr1:180555334-180555335
allele	A/G
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180553221..180556764-chr1:180577641..180580493,4	K562	blood:
2	chr1:180553413..180555386-chr1:180560751..180563747,2	K562	blood:
3	chr1:180554977..180557237-chr1:180558179..180559941,2	K562	blood:
4	chr1:180554771..180558903-chr1:180568895..180571854,4	K562	blood:
5	chr1:180553894..180556357-chr1:181120952..181123883,2	K562	blood:
6	chr1:180554937..180556534-chr1:180622491..180625409,2	K562	blood:
7	chr1:180530904..180533469-chr1:180554025..180555581,2	MCF-7	breast:
8	chr1:180548462..180550838-chr1:180552772..180555647,2	K562	blood:
9	chr1:180551712..180554824-chr1:180555012..180557601,3	K562	blood:
10	chr1:180550860..180552393-chr1:180552818..180555669,2	MCF-7	breast:
11	chr1:180550479..180555497-chr1:180560043..180567544,7	K562	blood:
12	chr1:180553661..180556688-chr1:180599992..180601805,3	MCF-7	breast:
13	chr1:180545102..180548047-chr1:180554770..180556756,2	MCF-7	breast:
14	chr1:180547494..180549201-chr1:180553238..180555932,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10494531	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073348	0.83[ASN][1000 genomes]
rs12077656	1.00[CHB][hapmap]
rs12723609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728004	0.83[AFR][1000 genomes]
rs12729441	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12735662	1.00[ASN][1000 genomes]
rs12754682	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16856420	1.00[CHB][hapmap]
rs17301118	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17373022	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17373133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845400	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663339	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72720941	1.00[ASN][1000 genomes]
rs72720943	1.00[ASN][1000 genomes]
rs72720953	1.00[ASN][1000 genomes]
rs72720958	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17301132	NT5C2	trans	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180549200-180555600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:180550600-180555800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:180551000-180555800	Weak transcription	HSMM	muscle
4	chr1:180553400-180556600	Enhancers	Placenta	Placenta
5	chr1:180553600-180557000	Enhancers	HepG2	liver
6	chr1:180554000-180556000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr1:180554000-180556200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:180554000-180556600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:180554000-180556600	Enhancers	Pancreas	Pancrea
10	chr1:180554000-180557000	Enhancers	HMEC	breast
11	chr1:180554000-180557200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:180554200-180555400	Enhancers	Fetal Thymus	thymus
13	chr1:180554200-180555800	Weak transcription	Esophagus	oesophagus
14	chr1:180554200-180556000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:180554200-180556000	Enhancers	NH-A	brain
16	chr1:180554200-180556600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:180554200-180556800	Enhancers	Osteobl	bone
18	chr1:180554400-180555600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:180554400-180556600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr1:180554600-180556000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:180554600-180556800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr1:180554600-180556800	Enhancers	A549	lung
23	chr1:180554800-180555400	Enhancers	Gastric	stomach
24	chr1:180554800-180555400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:180554800-180555400	Flanking Active TSS	NHEK	skin
26	chr1:180554800-180556000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:180554800-180556000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:180554800-180556000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:180554800-180556000	Flanking Active TSS	K562	blood
30	chr1:180554800-180556200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:180554800-180556200	Enhancers	Stomach Mucosa	stomach
32	chr1:180555000-180556600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:180555200-180555800	Weak transcription	HSMMtube	muscle
34	chr1:180555200-180556200	Enhancers	Dnd41	blood
35	chr1:180555200-180556400	Enhancers	Lung	lung
36	chr1:180555200-180556800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr1:180555200-180557000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links