Variant report

Variant	rs163327
Chromosome Location	chr3:161062724-161062725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:161001819..161012846-chr3:161052557..161065154,32	MCF-7	breast:
2	chr3:160944645..160947567-chr3:161062300..161064124,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10804790	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1154701	1.00[JPT][hapmap]
rs1382427	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1382428	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1478565	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1599374	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs1600209	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs163328	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs189270	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1993891	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28515190	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs336541	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs336543	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs336548	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs336567	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs336569	0.89[ASN][1000 genomes]
rs336570	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs336572	0.84[CEU][hapmap]
rs336577	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs336579	0.89[ASN][1000 genomes]
rs336580	0.84[CEU][hapmap]
rs336583	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs336585	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs336586	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs336589	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs336590	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs336591	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs336593	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs339101	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3849524	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[EUR][1000 genomes]
rs4273380	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4370045	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4414866	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4493449	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs456611	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4597724	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs460508	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs463928	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs464766	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6441373	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6762645	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6765269	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6774276	1.00[JPT][hapmap]
rs6775627	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs6789388	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs6794601	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs7611367	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7615592	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7623206	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7631479	0.85[CEU][hapmap]
rs7632797	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7633186	1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7638668	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7647327	0.80[EUR][1000 genomes]
rs7653361	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs975323	0.80[EUR][1000 genomes]
rs9790314	0.80[EUR][1000 genomes]
rs9821201	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9850455	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs9870059	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9872514	0.89[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv4091	chr3:161018540-161063875	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
5	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs163327	SPTSSB	cis	Thyroid	GTEx
rs163327	NMD3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161058200-161072200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:161058400-161067000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:161059200-161064400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:161059800-161089200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:161060600-161070200	Weak transcription	Esophagus	oesophagus
6	chr3:161061000-161063600	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr3:161061800-161063200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:161062200-161067400	Weak transcription	Gastric	stomach
9	chr3:161062400-161065400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:161062600-161067600	Weak transcription	HepG2	liver

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