Variant report

Variant	rs1333969
Chromosome Location	chr1:79090654-79090655
allele	C/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	WRNIP1	chr1:79090520-79090719	GM12878	blood:	n/a	n/a
2	CHD1	chr1:79090329-79090680	GM12878	blood:	n/a	n/a
3	RUNX3	chr1:79090391-79090723	GM12878	blood:	n/a	n/a
4	TBP	chr1:79090160-79090716	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:79090347-79090776	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:79088136-79090965	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:79084977-79091295	GM12891	blood:	n/a	n/a
8	RUNX3	chr1:79090373-79090824	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:79089094-79090888	GM12878	blood:	n/a	n/a
10	MAZ	chr1:79090324-79090777	GM12878	blood:	n/a	n/a
11	SIN3A	chr1:79090529-79090745	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
IFI44L	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11162518	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11162519	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12117719	0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12120385	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12136543	1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12738132	1.00[YRI][hapmap]
rs1413358	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17101968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35027639	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3818763	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820092	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs987495	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs988097	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][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	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1333969	PTGFR	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79086600-79091200	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr1:79086800-79090800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:79086800-79090800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr1:79086800-79092200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:79086800-79092800	Weak transcription	NHDF-Ad	bronchial
6	chr1:79086800-79092800	Weak transcription	Osteobl	bone
7	chr1:79086800-79108800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:79087200-79097400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:79088400-79094000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:79088600-79091200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:79088600-79110600	Weak transcription	Fetal Thymus	thymus
12	chr1:79088800-79090800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:79088800-79091000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:79088800-79092600	Weak transcription	Brain Substantia Nigra	brain
15	chr1:79088800-79095400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:79089000-79090800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:79089000-79095800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:79089400-79094200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:79089400-79094400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:79089400-79098800	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:79089400-79107200	Weak transcription	Ovary	ovary
22	chr1:79089600-79093600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:79089600-79098800	Weak transcription	Aorta	Aorta
24	chr1:79089800-79093600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:79089800-79115000	Weak transcription	Small Intestine	intestine
26	chr1:79090000-79091000	Weak transcription	Primary T cells from cord blood	blood
27	chr1:79090200-79092200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:79090400-79090800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
29	chr1:79090600-79090800	Enhancers	Adipose Nuclei	Adipose

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