Variant report

Variant	rs17101968
Chromosome Location	chr1:79102432-79102433
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11162518	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11162519	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12117719	0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12120385	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12136543	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333969	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]
rs1413358	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35027639	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818763	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820092	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs987495	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs988097	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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	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
3	nsv871140	chr1:79095581-79155134	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' 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
rs17101968	PTGFR	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79086800-79108800	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:79088600-79110600	Weak transcription	Fetal Thymus	thymus
3	chr1:79089400-79107200	Weak transcription	Ovary	ovary
4	chr1:79089800-79115000	Weak transcription	Small Intestine	intestine
5	chr1:79090800-79110000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:79090800-79110000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:79094400-79110600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:79094600-79110000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr1:79094600-79110200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:79094600-79115200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:79095000-79107200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:79097800-79103000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:79099200-79112800	Weak transcription	Lung	lung
14	chr1:79099400-79107200	Weak transcription	Aorta	Aorta
15	chr1:79099400-79107200	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:79101200-79103400	Strong transcription	GM12878-XiMat	blood
17	chr1:79101400-79109800	Weak transcription	Primary T cells from cord blood	blood
18	chr1:79101400-79115400	Weak transcription	Left Ventricle	heart
19	chr1:79102200-79114800	Weak transcription	Adipose Nuclei	Adipose

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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