Variant report

Variant	rs1147683
Chromosome Location	chr3:120083854-120083855
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	chr3:120073129..120075194-chr3:120083033..120085567,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1085612	0.84[AFR][1000 genomes]
rs1085613	0.84[AFR][1000 genomes]
rs1092829	0.84[AFR][1000 genomes]
rs1147682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1147686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147687	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1147702	0.92[CHD][hapmap]
rs1147704	1.00[ASW][hapmap];0.86[CEU][hapmap];0.88[CHD][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11708297	0.91[ASN][1000 genomes]
rs11713799	0.86[ASN][1000 genomes]
rs11717787	0.94[ASN][1000 genomes]
rs11718087	0.88[ASN][1000 genomes]
rs1259290	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1259295	0.82[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1259297	1.00[ASW][hapmap];0.82[CEU][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1259327	0.86[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs1356112	0.93[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs1588890	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1588891	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1606871	0.88[ASN][1000 genomes]
rs1606872	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1606873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1615793	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1617553	0.86[ASN][1000 genomes]
rs1621291	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1623323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16831067	0.87[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs16831087	0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs1716838	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1716839	0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1716840	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1716846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1733324	0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1733325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1733327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1733329	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1733331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1733353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1733354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2091727	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2138259	0.90[AFR][1000 genomes]
rs2638592	0.84[AFR][1000 genomes]
rs2673696	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2673701	0.86[ASN][1000 genomes]
rs2673704	1.00[ASW][hapmap];0.82[CEU][hapmap];0.81[GIH][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2700260	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2702156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2702157	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2702158	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2702164	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2943754	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438576	1.00[ASW][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6438578	1.00[ASW][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6438579	0.90[AFR][1000 genomes]
rs7616519	0.82[ASN][1000 genomes]
rs7616807	0.87[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7622363	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs7639144	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs787197	0.83[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs787201	0.86[CHB][hapmap]
rs787210	0.84[AFR][1000 genomes]
rs916509	0.82[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs916512	0.82[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs939499	0.90[AFR][1000 genomes]
rs950649	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs950650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1147683	PDIA5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120083200-120084600	Enhancers	Fetal Thymus	thymus
2	chr3:120083400-120084200	Enhancers	Muscle Satellite Cultured Cells	--
3	chr3:120083400-120084200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:120083400-120084400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:120083400-120084600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:120083600-120084000	Enhancers	HMEC	breast
7	chr3:120083600-120084200	Enhancers	HSMM	muscle
8	chr3:120083600-120084200	Enhancers	NHDF-Ad	bronchial
9	chr3:120083800-120084000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:120083800-120084200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links