Variant report

Variant	rs6504067
Chromosome Location	chr17:46219204-46219205
allele	C/G
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	chr17:46218896-46219546	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:46219108-46219343	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SKAP1	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11079810	0.89[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11079813	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11650476	0.90[EUR][1000 genomes]
rs11650615	0.92[YRI][hapmap]
rs11654292	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11654342	0.84[AMR][1000 genomes]
rs11658242	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12103808	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1544597	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1975703	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs28481675	0.90[EUR][1000 genomes]
rs56258199	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60707285	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60843764	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6504114	1.00[CEU][hapmap];0.89[YRI][hapmap];0.90[EUR][1000 genomes]
rs6504115	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs7207553	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7207937	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7210671	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7219844	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7220398	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7221720	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7221897	0.82[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7222646	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7224155	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7225288	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73322881	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73322886	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73324779	0.90[EUR][1000 genomes]
rs8065797	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs8067470	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs8071697	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8073220	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9890850	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9893110	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9894076	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9900074	0.85[YRI][hapmap]
rs9905800	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9907268	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9909922	0.88[AMR][1000 genomes];0.81[EUR][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	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
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6504067	RP5-890E16.2	cis	Nerve Tibial	GTEx
rs6504067	PNPO	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46191200-46220800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:46197800-46221000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr17:46200400-46236600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr17:46204000-46220000	Weak transcription	GM12878-XiMat	blood
5	chr17:46204200-46225200	Weak transcription	Liver	Liver
6	chr17:46204400-46221000	Weak transcription	Thymus	Thymus
7	chr17:46206400-46220800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:46210000-46224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr17:46211200-46231600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:46212400-46234800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr17:46213400-46220800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:46215400-46225400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr17:46216600-46235600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr17:46216800-46219600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr17:46217000-46219800	Strong transcription	Primary T cells from cord blood	blood
17	chr17:46217600-46220200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr17:46217600-46221600	Strong transcription	Fetal Thymus	thymus
19	chr17:46218000-46220000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr17:46218000-46220000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr17:46218000-46220800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr17:46218000-46224200	Weak transcription	Primary B cells from cord blood	blood
23	chr17:46218200-46221800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr17:46218200-46224800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr17:46219000-46220000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr17:46219200-46219400	Enhancers	Esophagus	oesophagus
27	chr17:46219200-46219600	Bivalent Enhancer	HepG2	liver

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