Variant report

Variant	rs17301118
Chromosome Location	chr1:180553402-180553403
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: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	chr1:180553221..180556764-chr1:180577641..180580493,4	K562	blood:
2	chr1:180551712..180554824-chr1:180555012..180557601,3	K562	blood:
3	chr1:180552648..180554926-chr1:180634516..180636719,2	K562	blood:
4	chr1:180546286..180547844-chr1:180551705..180553477,2	K562	blood:
5	chr1:180548462..180550838-chr1:180552772..180555647,2	K562	blood:
6	chr1:180550860..180552393-chr1:180552818..180555669,2	MCF-7	breast:
7	chr1:180550479..180555497-chr1:180560043..180567544,7	K562	blood:
8	chr1:180490294..180492192-chr1:180552011..180554702,2	MCF-7	breast:
9	chr1:180552650..180554961-chr1:180564277..180566227,2	K562	blood:
10	chr1:180552552..180554229-chr1:180589364..180592106,2	MCF-7	breast:
11	chr1:180547494..180549201-chr1:180553238..180555932,2	MCF-7	breast:

No data

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];0.88[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];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12728004	0.95[AFR][1000 genomes]
rs12729441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12735662	1.00[ASN][1000 genomes]
rs12754682	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs16856420	1.00[CHB][hapmap]
rs17301132	1.00[CEU][hapmap];1.00[CHB][hapmap];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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845400	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.86[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
rs17301118	NT5C2	trans	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180549200-180555600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:180549400-180554800	Weak transcription	Stomach Mucosa	stomach
3	chr1:180549800-180553800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:180549800-180554800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:180550000-180554000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:180550200-180554000	Weak transcription	NHEK	skin
7	chr1:180550400-180554800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:180550600-180555800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:180550800-180554000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:180550800-180554000	Weak transcription	Pancreas	Pancrea
11	chr1:180551000-180553600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:180551000-180554000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:180551000-180554000	Weak transcription	HMEC	breast
14	chr1:180551000-180554600	Weak transcription	HSMMtube	muscle
15	chr1:180551000-180555800	Weak transcription	HSMM	muscle
16	chr1:180551200-180554000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:180551200-180554000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:180551200-180554200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:180551200-180554200	Weak transcription	NH-A	brain
20	chr1:180551200-180554400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:180551200-180554600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr1:180551400-180554000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:180551400-180554200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:180551400-180554800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:180552000-180554200	Weak transcription	Osteobl	bone
26	chr1:180553400-180553800	Enhancers	K562	blood
27	chr1:180553400-180556600	Enhancers	Placenta	Placenta

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