Variant report

Variant	rs1046938
Chromosome Location	chr3:156978173-156978174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10451871	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10451916	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10513507	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1060543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1157738	0.87[CEU][hapmap]
rs11926167	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637518	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12696045	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081038	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13084070	0.80[ASN][1000 genomes]
rs13084522	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1392799	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1403103	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1403104	0.88[CEU][hapmap];0.95[TSI][hapmap]
rs1500925	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1587534	0.81[EUR][1000 genomes]
rs1587535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1608127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16827308	0.88[CEU][hapmap]
rs16827322	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs16827350	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16827384	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35217153	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3749214	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4383468	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4632503	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4679788	0.83[CEU][hapmap]
rs4680342	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4680344	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4680346	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680347	0.91[CEU][hapmap]
rs4680348	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6441114	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6441122	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767619	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6773061	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6780831	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6781991	0.80[ASN][1000 genomes]
rs6783595	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs6789178	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6805114	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6808284	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6808457	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809003	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.80[ASN][1000 genomes]
rs6809394	0.88[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.80[ASN][1000 genomes]
rs7620178	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7625059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636185	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7638194	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7642179	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7647643	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs924517	0.91[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9289978	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289979	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289980	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9811195	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9827676	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9831830	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9848409	0.80[ASN][1000 genomes]
rs9849168	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861469	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9867618	0.91[MEX][hapmap];0.84[TSI][hapmap]

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	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv877687	chr3:156924793-157044184	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1046938	PTX3	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156967000-156979000	Weak transcription	HSMMtube	muscle
2	chr3:156967200-156982000	Weak transcription	Lung	lung
3	chr3:156967200-156989000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:156967200-157000000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:156967200-157000000	Weak transcription	NH-A	brain
6	chr3:156967200-157007800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:156968000-156981800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:156972800-156978400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:156974000-156982400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:156974200-156979000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:156975200-156979600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:156975200-156980600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:156975400-156978400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:156975400-156978400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:156975400-156980600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:156975600-156978800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:156975600-156980400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:156975600-156980400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:156975600-156980800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:156975800-156978200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:156976600-156980400	Weak transcription	HUVEC	blood vessel
22	chr3:156977200-156980600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:156977800-156982000	Enhancers	Osteobl	bone
24	chr3:156978000-156979000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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