Variant report

Variant	rs9890096
Chromosome Location	chr17:46097083-46097084
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46048202..46050216-chr17:46095604..46097333,2	MCF-7	breast:
2	chr17:46097069..46099255-chr17:46124273..46125905,2	MCF-7	breast:
3	chr17:46094248..46097209-chr17:46632627..46635464,2	K562	blood:
4	chr17:46048492..46050291-chr17:46095854..46098478,2	MCF-7	breast:
5	chr17:46095774..46097363-chr17:46099582..46101725,2	MCF-7	breast:
6	chr17:46046870..46049794-chr17:46095106..46097466,2	K562	blood:
7	chr17:46091408..46093930-chr17:46096491..46098890,2	MCF-7	breast:
8	chr17:46058567..46062223-chr17:46094441..46097254,3	K562	blood:
9	chr17:46094604..46097136-chr17:46099608..46102510,2	K562	blood:
10	chr17:46027110..46029262-chr17:46094448..46097370,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000263412	Chromatin interaction
ENSG00000239552	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000120093	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10491182	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10491183	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1051001	0.88[EUR][1000 genomes]
rs11079805	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11651275	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11656818	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12452399	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28405789	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35091825	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs41429650	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7209072	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7210041	0.86[EUR][1000 genomes]
rs9895554	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9900074	0.90[EUR][1000 genomes]
rs9903963	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9914123	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9890096	PNPO	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46090200-46100400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr17:46090200-46100400	Weak transcription	Brain Substantia Nigra	brain
3	chr17:46090400-46100800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:46092600-46100400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr17:46092600-46100800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr17:46092600-46100800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr17:46092800-46100200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr17:46092800-46100400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr17:46092800-46100600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr17:46092800-46100600	Weak transcription	Fetal Brain Female	brain
11	chr17:46093800-46100600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr17:46094000-46098600	Weak transcription	HSMMtube	muscle
13	chr17:46094000-46100400	Weak transcription	HSMM	muscle
14	chr17:46094000-46101600	Weak transcription	K562	blood
15	chr17:46095800-46097600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr17:46095800-46098800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:46095800-46100200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr17:46095800-46100200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr17:46095800-46100200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr17:46095800-46100400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr17:46095800-46100400	Weak transcription	A549	lung
22	chr17:46095800-46100600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:46095800-46100600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr17:46095800-46100600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr17:46096000-46098200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr17:46096000-46100400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr17:46096000-46100600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr17:46096400-46098000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr17:46096800-46097800	Weak transcription	Brain Germinal Matrix	brain

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