Variant report

Variant	rs12489030
Chromosome Location	chr3:99696469-99696470
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	chr3:99695276..99697068-chr3:99707515..99710288,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1038295	0.87[ASN][1000 genomes]
rs10804762	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485299	0.83[ASN][1000 genomes]
rs12486901	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491153	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs12493124	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs12493320	1.00[CEU][hapmap]
rs12494994	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs12496041	0.83[AFR][1000 genomes]
rs1492343	0.83[ASN][1000 genomes]
rs1565341	0.84[CHB][hapmap];0.80[CHD][hapmap];0.88[JPT][hapmap]
rs1871847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35590972	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732444	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3921767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928222	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4928233	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs4928236	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs55874130	0.95[EUR][1000 genomes]
rs55881709	0.91[EUR][1000 genomes]
rs55964918	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140081	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56223679	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260910	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56335268	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60119031	0.90[ASN][1000 genomes]
rs61010376	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440991	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6777622	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6778589	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6792339	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73858966	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73859911	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73860464	0.83[ASN][1000 genomes]
rs73860470	0.86[ASN][1000 genomes]
rs7431827	0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs7610759	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs7632345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634628	0.84[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs7635633	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7635871	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7652706	0.82[YRI][hapmap]
rs9824430	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs9827744	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs9872339	0.82[ASW][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99677400-99696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:99679600-99697000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:99689200-99697400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:99689800-99702000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:99690600-99697400	Weak transcription	Psoas Muscle	Psoas
6	chr3:99693000-99699600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:99694200-99699800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:99694400-99699600	Weak transcription	Left Ventricle	heart

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