Variant report

Variant	rs10802777
Chromosome Location	chr1:239750392-239750393
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10127769	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754673	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10754674	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754675	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802776	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802778	0.94[ASN][1000 genomes]
rs10802779	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802780	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10925916	0.90[EUR][1000 genomes]
rs10925918	0.90[ASN][1000 genomes]
rs10925920	0.98[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10925921	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10925924	0.83[ASN][1000 genomes]
rs10925926	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12089818	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118974	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12123624	0.88[EUR][1000 genomes]
rs12402224	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416378	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1416379	0.88[EUR][1000 genomes]
rs1538442	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1867262	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4376722	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507997	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4659547	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4659920	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670526	0.88[EUR][1000 genomes]
rs6670728	0.88[EUR][1000 genomes]
rs7526165	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs997148	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997538	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10802777	PTGS2	trans	brain	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239728800-239769400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:239743800-239750400	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:239744000-239761400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:239746400-239756200	Weak transcription	Gastric	stomach
5	chr1:239746600-239757600	Weak transcription	Pancreas	Pancrea
6	chr1:239747000-239754600	Weak transcription	Fetal Kidney	kidney
7	chr1:239747400-239750800	Weak transcription	Fetal Intestine Small	intestine
8	chr1:239747400-239753400	Weak transcription	Ovary	ovary
9	chr1:239748600-239751000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:239748600-239751000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:239749000-239750400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:239749400-239750400	Weak transcription	Primary T cells from cord blood	blood
13	chr1:239750000-239750600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:239750200-239750600	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr1:239750200-239750800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:239750200-239751000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:239750200-239751200	Enhancers	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links