Variant report

Variant	rs1392798
Chromosome Location	chr3:157056287-157056288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1014855	0.84[MEX][hapmap]
rs10936079	0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10936088	0.88[MEX][hapmap]
rs12486955	0.91[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12494423	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[TSI][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12636252	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1456104	0.87[MEX][hapmap]
rs1456110	0.84[CEU][hapmap]
rs1500921	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1500923	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1522393	0.86[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.83[ASN][1000 genomes]
rs1566521	0.82[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1581413	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1869857	0.84[CEU][hapmap]
rs28638274	0.84[CEU][hapmap]
rs34263112	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4640513	0.84[CEU][hapmap]
rs56311637	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62278578	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62278580	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73156728	0.81[ASN][1000 genomes]
rs7642909	0.85[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs991083	0.83[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1392798	PTX3	cis	cerebellum	SCAN
rs1392798	BRD7	cis	cerebellum	SCAN
rs1392798	SSR3	cis	cerebellum	SCAN
rs1392798	MXRA7	trans	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157041000-157065600	Weak transcription	Pancreas	Pancrea
2	chr3:157048200-157057000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:157054400-157056600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:157054400-157057200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:157054400-157058000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:157054600-157056600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:157054600-157056600	Weak transcription	NHDF-Ad	bronchial
8	chr3:157054600-157056800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:157054600-157057000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:157054800-157065200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:157055400-157057200	Weak transcription	A549	lung
12	chr3:157055800-157065600	Weak transcription	Osteobl	bone
13	chr3:157056200-157072600	Weak transcription	HUVEC	blood vessel

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