Variant report

Variant	rs6799567
Chromosome Location	chr3:157019103-157019104
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10460861	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10513508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10513509	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs10513510	0.86[CHB][hapmap];0.82[TSI][hapmap]
rs10513512	0.86[CHB][hapmap];0.89[GIH][hapmap];0.82[TSI][hapmap]
rs10804778	0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs10936063	0.91[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs10936066	0.91[CEU][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs10936074	0.81[AMR][1000 genomes]
rs10936075	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10936077	0.91[CHB][hapmap]
rs10936078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10936080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10936081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10936083	1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs1157738	0.82[CEU][hapmap]
rs11918974	0.91[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs12488480	0.90[CEU][hapmap];0.92[JPT][hapmap]
rs12490120	0.82[CHB][hapmap]
rs12490192	0.86[ASN][1000 genomes]
rs12492801	0.91[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs12493531	0.85[AMR][1000 genomes]
rs12494465	0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs12495519	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12496051	0.82[AMR][1000 genomes]
rs12496111	0.90[CEU][hapmap];0.84[JPT][hapmap]
rs12496269	0.80[ASN][1000 genomes]
rs12629589	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12632525	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12632562	0.86[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12633429	0.91[CEU][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12634054	0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs12634689	0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs12634818	0.82[AMR][1000 genomes]
rs12635316	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636125	0.84[JPT][hapmap]
rs12637476	0.95[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1403104	0.82[MEX][hapmap]
rs1403106	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1403108	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1403109	0.83[CHB][hapmap]
rs1456109	0.81[CHB][hapmap]
rs1474281	0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs1500917	0.86[CHB][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs1500918	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs1500922	0.82[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap]
rs1500924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1522392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1546260	0.83[CHB][hapmap]
rs1568611	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16827352	0.82[AMR][1000 genomes]
rs16827483	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16827516	0.88[ASN][1000 genomes]
rs16827530	0.86[ASN][1000 genomes]
rs1875315	0.88[ASN][1000 genomes]
rs1995304	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs2047648	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2173824	0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs2321742	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2874616	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35910014	0.82[AMR][1000 genomes]
rs3935750	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs4679788	0.94[CEU][hapmap];0.83[JPT][hapmap]
rs4679789	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4680340	0.91[CEU][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs4680343	0.90[CEU][hapmap];0.84[JPT][hapmap]
rs4680345	0.90[CEU][hapmap]
rs4680349	0.96[AMR][1000 genomes]
rs4680352	0.90[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4680354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5003893	0.91[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs55865575	0.86[ASN][1000 genomes]
rs55949516	0.82[AMR][1000 genomes]
rs55953639	0.82[AMR][1000 genomes]
rs56143236	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56150358	0.88[AMR][1000 genomes]
rs56313302	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59279023	0.82[AMR][1000 genomes]
rs61149035	0.81[AMR][1000 genomes]
rs62276490	0.82[AMR][1000 genomes]
rs62276491	0.81[AMR][1000 genomes]
rs62276495	0.82[AMR][1000 genomes]
rs62276496	0.81[AMR][1000 genomes]
rs62276497	0.81[AMR][1000 genomes]
rs62276502	0.82[AMR][1000 genomes]
rs62276505	0.82[AMR][1000 genomes]
rs62276528	0.85[AMR][1000 genomes]
rs62278575	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62278582	0.86[ASN][1000 genomes]
rs62278584	0.86[ASN][1000 genomes]
rs62278585	0.86[ASN][1000 genomes]
rs62278586	0.85[ASN][1000 genomes]
rs62278596	0.84[ASN][1000 genomes]
rs62278597	0.86[ASN][1000 genomes]
rs62278598	0.86[ASN][1000 genomes]
rs62281377	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62281379	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62281383	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6441115	0.91[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs6441116	0.91[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs6768074	0.91[CEU][hapmap];0.83[JPT][hapmap]
rs6780205	0.81[AMR][1000 genomes]
rs6781682	0.87[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs6788214	0.88[CEU][hapmap]
rs6805989	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs6809307	0.91[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs73154657	0.82[AMR][1000 genomes]
rs73154671	0.94[AMR][1000 genomes]
rs73154682	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73156756	0.86[ASN][1000 genomes]
rs73156757	0.85[ASN][1000 genomes]
rs7610214	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7619892	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7621912	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs7626589	0.82[AMR][1000 genomes]
rs7631257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648599	0.91[CEU][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs7649737	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7652298	0.91[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8925	0.91[CEU][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs924516	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs949854	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6799567	PTX3	cis	parietal	SCAN
rs6799567	SMC4	cis	parietal	SCAN
rs6799567	PTX3	cis	cerebellum	SCAN
rs6799567	CCNL1	cis	multi-tissue	Pritchard
rs6799567	IL12A	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157004800-157028200	Weak transcription	HUVEC	blood vessel
2	chr3:157013000-157032600	Weak transcription	NH-A	brain
3	chr3:157013200-157019600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:157014400-157019200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:157015400-157019600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:157015600-157048400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:157017400-157019200	Enhancers	Osteobl	bone
8	chr3:157017400-157019400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr3:157017400-157019400	Enhancers	NHDF-Ad	bronchial
10	chr3:157017600-157019200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:157018200-157020200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:157018600-157019200	Flanking Active TSS	K562	blood
13	chr3:157018800-157019200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:157019000-157019200	Enhancers	HSMMtube	muscle
15	chr3:157019000-157029000	Weak transcription	NHLF	lung

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