Variant report

Variant	rs7639254
Chromosome Location	chr3:157141041-157141042
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1027603	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs10936085	0.94[CHB][hapmap]
rs10936086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936087	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12486427	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12492874	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12492929	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12496879	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs12629552	0.83[ASN][1000 genomes]
rs12636038	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12638732	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13087207	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1456097	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1456105	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1456106	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1456108	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1456110	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs1500916	0.95[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.82[ASN][1000 genomes]
rs1500920	0.87[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs1545596	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1546261	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs1563420	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1568609	0.91[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap]
rs1568612	0.83[CHB][hapmap]
rs1585080	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1824058	0.95[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs1840668	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1840673	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[GIH][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1869857	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs1869859	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1965246	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2047649	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2085315	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124497	0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2168430	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2168431	0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2305620	0.92[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2305622	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28638274	0.80[CEU][hapmap];0.83[TSI][hapmap]
rs35004310	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816527	0.90[JPT][hapmap]
rs3816528	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435581	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4640512	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640513	0.80[CEU][hapmap]
rs4679793	0.95[CEU][hapmap];0.89[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4680351	0.83[CHB][hapmap]
rs4680359	0.94[CHB][hapmap]
rs4680360	0.91[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680367	0.82[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap]
rs6441126	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441127	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441128	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441129	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6776647	0.83[CHB][hapmap]
rs6801110	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs6803628	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs722484	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7614339	0.87[CHB][hapmap]
rs7617727	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618737	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7623173	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7626884	0.82[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7629293	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7631556	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs7634847	0.80[ASN][1000 genomes]
rs9857875	0.95[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs9871290	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9878474	0.95[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9883103	0.84[CHB][hapmap]
rs988587	0.95[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs988588	0.95[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap]
rs9990136	0.95[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[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	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7639254	PTX3	cis	cerebellum	SCAN
rs7639254	SSR3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157091800-157142600	Weak transcription	Pancreas	Pancrea
2	chr3:157119000-157142800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:157120000-157142600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:157127000-157141800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:157136000-157142800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:157136200-157145800	Weak transcription	NHLF	lung
7	chr3:157136200-157146800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:157139000-157154600	Weak transcription	Lung	lung
9	chr3:157139600-157142800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:157140600-157141600	Enhancers	HSMMtube	muscle
11	chr3:157140800-157141800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:157140800-157142000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:157141000-157141400	Enhancers	NH-A	brain
14	chr3:157141000-157141600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:157141000-157141800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:157141000-157141800	Enhancers	HSMM	muscle
17	chr3:157141000-157141800	Enhancers	HUVEC	blood vessel
18	chr3:157141000-157141800	Enhancers	NHDF-Ad	bronchial
19	chr3:157141000-157141800	Enhancers	Osteobl	bone

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