Variant report

Variant	rs16827322
Chromosome Location	chr3:156950878-156950879
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156869339..156870911-chr3:156949584..156952069,2	K562	blood:
2	chr3:156950469..156951990-chr3:156955060..156957422,2	K562	blood:

Variant related genes	Relation type
ENSG00000163660	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10451916	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs1046938	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs10513507	0.88[CEU][hapmap]
rs1060543	0.87[CEU][hapmap]
rs10804777	0.82[CHB][hapmap]
rs10936063	0.87[CEU][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap]
rs10936066	0.87[CEU][hapmap];0.87[MKK][hapmap]
rs10936067	0.88[AMR][1000 genomes]
rs10936068	0.90[AMR][1000 genomes]
rs10936069	0.86[AMR][1000 genomes]
rs10936074	0.85[AMR][1000 genomes]
rs1157738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12488480	0.86[CEU][hapmap]
rs12489453	0.87[AMR][1000 genomes]
rs12489799	0.87[AMR][1000 genomes]
rs12490836	0.87[AMR][1000 genomes]
rs12492801	0.87[CEU][hapmap];0.87[MKK][hapmap]
rs12493531	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496051	0.90[AMR][1000 genomes]
rs12496111	0.85[CEU][hapmap];0.88[AMR][1000 genomes]
rs12632562	0.82[CEU][hapmap]
rs12633429	0.87[CEU][hapmap];0.87[MKK][hapmap]
rs12634818	0.90[AMR][1000 genomes]
rs12637932	0.82[CHB][hapmap]
rs13061214	0.91[CEU][hapmap]
rs13081036	0.92[CEU][hapmap]
rs13081038	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs1392799	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs1403104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1403106	0.87[CEU][hapmap]
rs1587535	0.88[CEU][hapmap]
rs1608127	0.92[CEU][hapmap]
rs16827308	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16827318	0.88[AMR][1000 genomes]
rs16827352	0.90[AMR][1000 genomes]
rs1969066	0.86[EUR][1000 genomes]
rs1995304	0.87[CEU][hapmap];0.88[AMR][1000 genomes]
rs2321740	0.83[AMR][1000 genomes]
rs2874616	0.87[CEU][hapmap]
rs35910014	0.90[AMR][1000 genomes]
rs3749214	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs3935750	0.87[CEU][hapmap]
rs4256081	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4413278	0.84[AMR][1000 genomes]
rs4679788	0.83[CEU][hapmap];0.87[AMR][1000 genomes]
rs4680340	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs4680342	0.81[CEU][hapmap]
rs4680343	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs4680345	0.86[CEU][hapmap];0.82[AMR][1000 genomes]
rs4680346	0.87[CEU][hapmap]
rs4680347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680352	0.87[CEU][hapmap]
rs5003893	0.87[CEU][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap]
rs55828309	0.80[AMR][1000 genomes]
rs55835412	0.90[AMR][1000 genomes]
rs55949516	0.90[AMR][1000 genomes]
rs55953639	0.90[AMR][1000 genomes]
rs56078410	0.88[AMR][1000 genomes]
rs56263456	0.88[AMR][1000 genomes]
rs57322659	0.88[AMR][1000 genomes]
rs57511361	0.88[AMR][1000 genomes]
rs58666615	0.91[EUR][1000 genomes]
rs59279023	0.90[AMR][1000 genomes]
rs59485606	0.90[AMR][1000 genomes]
rs60153077	0.88[AMR][1000 genomes]
rs61149035	0.89[AMR][1000 genomes]
rs62274159	0.80[AMR][1000 genomes]
rs62276465	0.86[AMR][1000 genomes]
rs62276470	0.88[AMR][1000 genomes]
rs62276471	0.90[AMR][1000 genomes]
rs62276474	0.90[AMR][1000 genomes]
rs62276475	0.90[AMR][1000 genomes]
rs62276479	0.88[AMR][1000 genomes]
rs62276480	0.88[AMR][1000 genomes]
rs62276488	0.81[AMR][1000 genomes]
rs62276489	0.90[AMR][1000 genomes]
rs62276490	0.88[AMR][1000 genomes]
rs62276491	0.87[AMR][1000 genomes]
rs62276493	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276495	0.88[AMR][1000 genomes]
rs62276496	0.87[AMR][1000 genomes]
rs62276497	0.89[AMR][1000 genomes]
rs62276501	0.87[AMR][1000 genomes]
rs62276502	0.90[AMR][1000 genomes]
rs62276504	0.87[AMR][1000 genomes]
rs62276505	0.90[AMR][1000 genomes]
rs62276528	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6441115	0.87[CEU][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap]
rs6441116	0.87[CEU][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap]
rs6441119	0.84[AMR][1000 genomes]
rs6441123	0.87[CEU][hapmap]
rs6767619	0.91[CEU][hapmap]
rs6768052	0.88[AMR][1000 genomes]
rs6768074	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs6780205	0.85[AMR][1000 genomes]
rs6781682	0.83[CEU][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.82[AMR][1000 genomes]
rs6788214	0.84[CEU][hapmap]
rs6792479	0.88[AMR][1000 genomes]
rs6805114	0.82[CEU][hapmap]
rs6805989	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs6806232	0.80[AMR][1000 genomes]
rs6808457	0.87[CEU][hapmap]
rs6809003	0.81[CEU][hapmap];0.90[TSI][hapmap]
rs6809307	0.87[CEU][hapmap];0.87[MEX][hapmap]
rs6809394	0.80[CEU][hapmap];0.88[TSI][hapmap]
rs68122740	0.96[EUR][1000 genomes]
rs73154649	0.87[AMR][1000 genomes]
rs73154652	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73154657	0.90[AMR][1000 genomes]
rs73154659	0.87[AMR][1000 genomes]
rs73873800	0.88[AMR][1000 genomes]
rs7621912	0.87[CEU][hapmap];0.80[AMR][1000 genomes]
rs7625059	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs7626589	0.90[AMR][1000 genomes]
rs7638194	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs7647643	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs7648599	0.87[CEU][hapmap];0.87[MKK][hapmap];0.88[AMR][1000 genomes]
rs7652298	0.87[CEU][hapmap]
rs872652	0.82[CHB][hapmap]
rs8925	0.87[CEU][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap]
rs9827676	0.81[CEU][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16827322	SMC4	cis	parietal	SCAN
rs16827322	PTX3	cis	parietal	SCAN
rs16827322	CCNL1	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156949400-156952400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:156949600-156956800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:156950000-156955600	Weak transcription	Osteobl	bone
4	chr3:156950400-156952400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:156950600-156957000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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