Variant report

Variant	rs1733324
Chromosome Location	chr3:120103009-120103010
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	chr3:120100086..120101998-chr3:120102835..120104694,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1147683	0.86[ASN][1000 genomes]
rs1147686	0.86[ASN][1000 genomes]
rs1147687	0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1147691	0.86[ASN][1000 genomes]
rs1147692	0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1147702	0.92[CHD][hapmap];0.81[ASN][1000 genomes]
rs1147704	0.88[CHD][hapmap]
rs11708297	0.93[ASN][1000 genomes]
rs11713799	0.95[ASN][1000 genomes]
rs11717787	0.83[ASN][1000 genomes]
rs11718087	0.93[ASN][1000 genomes]
rs1259290	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs1259291	0.81[AMR][1000 genomes]
rs1259293	0.82[CEU][hapmap]
rs1356112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1588890	0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs1588891	0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1606871	0.93[ASN][1000 genomes]
rs1606872	0.84[ASN][1000 genomes]
rs1606873	0.81[ASN][1000 genomes]
rs1615793	0.90[ASN][1000 genomes]
rs1617553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1621291	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs1623323	0.88[ASN][1000 genomes]
rs16831067	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16831087	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1716838	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1716840	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.96[ASN][1000 genomes]
rs1716846	0.86[ASN][1000 genomes]
rs1733325	0.90[ASN][1000 genomes]
rs1733327	0.90[ASN][1000 genomes]
rs1733329	0.93[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1733331	0.85[ASN][1000 genomes]
rs1733353	0.88[ASN][1000 genomes]
rs1733354	0.88[ASN][1000 genomes]
rs2091727	0.94[ASN][1000 genomes]
rs2673696	0.93[ASN][1000 genomes]
rs2673701	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2702156	0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2702157	0.93[ASN][1000 genomes]
rs2702158	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs2702164	0.90[ASN][1000 genomes]
rs2943754	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4676697	0.83[JPT][hapmap]
rs6438576	0.86[CHB][hapmap]
rs6438578	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs7616519	0.95[ASN][1000 genomes]
rs7616807	0.93[CHB][hapmap];0.87[JPT][hapmap];0.95[ASN][1000 genomes]
rs7622363	0.86[CHB][hapmap]
rs7639144	0.93[ASN][1000 genomes]
rs787201	0.91[CEU][hapmap]
rs950649	0.84[ASN][1000 genomes]
rs950650	0.86[ASN][1000 genomes]
rs9851825	0.91[CEU][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv3968	chr3:120066454-120111463	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1733324	C3orf1	cis	parietal	SCAN
rs1733324	GPR156	cis	Esophagus Muscularis	GTEx
rs1733324	CD80	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120090600-120112600	Weak transcription	Aorta	Aorta
2	chr3:120096800-120112600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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