Variant report

Variant	rs9903963
Chromosome Location	chr17:46121228-46121229
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:46121213-46121248	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:46120283-46121360	K562	blood:	n/a	n/a
3	POLR2A	chr17:46120258-46121281	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46120967..46123256-chr17:46183656..46186285,2	MCF-7	breast:
2	chr17:46120800..46123915-chr17:46177973..46180193,3	MCF-7	breast:
3	chr17:46117511..46121845-chr17:46183690..46186313,3	MCF-7	breast:

Variant related genes	Relation type
NFE2L1	TF binding region
ENSG00000002919	Chromatin interaction
ENSG00000108468	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10491182	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491183	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1051001	0.96[EUR][1000 genomes]
rs11079805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11650043	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs11651275	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11656818	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12051	0.84[YRI][hapmap]
rs12452399	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969990	1.00[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap]
rs17617360	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs17618704	1.00[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap]
rs17679445	1.00[CEU][hapmap]
rs28405789	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35091825	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41429650	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4378657	0.87[GIH][hapmap]
rs7209072	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7210041	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs9890096	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9895554	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9900074	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9914123	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[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
rs9903963	PNPO	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46115600-46123800	Weak transcription	Brain Substantia Nigra	brain
2	chr17:46115800-46122600	Weak transcription	Esophagus	oesophagus
3	chr17:46115800-46122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr17:46115800-46122800	Weak transcription	Brain Anterior Caudate	brain
5	chr17:46115800-46122800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:46115800-46123200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:46115800-46123200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr17:46116000-46122600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr17:46116000-46122600	Weak transcription	NH-A	brain
10	chr17:46116000-46123000	Weak transcription	NHLF	lung
11	chr17:46116000-46124000	Weak transcription	Brain Hippocampus Middle	brain
12	chr17:46117000-46122600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:46119200-46121400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr17:46119400-46123400	Weak transcription	A549	lung
15	chr17:46119400-46123800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr17:46120200-46121400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr17:46120200-46121400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr17:46120200-46121400	Enhancers	NHEK	skin
19	chr17:46120200-46121600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr17:46120200-46121800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:46120200-46122600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr17:46120200-46122800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:46120200-46123000	Enhancers	NHDF-Ad	bronchial
24	chr17:46120400-46121400	Enhancers	HSMMtube	muscle
25	chr17:46120400-46121400	Enhancers	Osteobl	bone
26	chr17:46120400-46121600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr17:46120400-46121600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr17:46120400-46122600	Enhancers	HSMM	muscle
29	chr17:46120600-46121400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:46120600-46122600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr17:46120600-46122800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr17:46120600-46124200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr17:46120600-46124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr17:46120800-46122400	Weak transcription	Psoas Muscle	Psoas
35	chr17:46120800-46122600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:46120800-46122800	Weak transcription	Placenta	Placenta
37	chr17:46121000-46121400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr17:46121000-46122600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr17:46121200-46122600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr17:46121200-46122600	Weak transcription	HMEC	breast
41	chr17:46121200-46122600	Weak transcription	K562	blood
42	chr17:46121200-46123400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links