Variant report

Variant	rs12185989
Chromosome Location	chr3:23363050-23363051
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	chr3:23361011..23363823-chr3:23364424..23367156,3	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10451986	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10510536	0.89[YRI][hapmap]
rs11129112	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11129114	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11916447	0.82[ASN][1000 genomes]
rs11921580	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11928344	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12630883	0.84[ASN][1000 genomes]
rs12633613	0.84[ASN][1000 genomes]
rs12634459	0.83[AMR][1000 genomes]
rs12636682	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1495135	0.81[ASN][1000 genomes]
rs17341838	1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[ASN][1000 genomes]
rs17343818	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17403650	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1826847	0.83[AMR][1000 genomes]
rs1908772	0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs2172827	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2359637	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2359638	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28370926	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2884787	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4368441	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4553929	0.83[AMR][1000 genomes]
rs55895449	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs55934161	0.84[AMR][1000 genomes]
rs57055494	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57234542	0.84[AMR][1000 genomes]
rs57575542	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs57624654	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57869672	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60407944	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6550761	0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs6762615	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6763074	0.84[AMR][1000 genomes]
rs6764047	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6765562	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6766166	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6771053	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6771206	0.84[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6773311	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6776770	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6778478	0.90[JPT][hapmap];0.83[AMR][1000 genomes]
rs6792462	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6797467	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6807390	0.83[AMR][1000 genomes]
rs6807788	0.90[JPT][hapmap]
rs73033545	0.83[ASN][1000 genomes]
rs73033551	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7428484	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7610906	0.85[JPT][hapmap]
rs7610971	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7611132	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7613733	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7613969	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7614926	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7617659	0.81[AMR][1000 genomes]
rs7622913	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7632520	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7635784	0.84[ASN][1000 genomes]
rs7636536	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7638278	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7638405	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7640458	0.85[JPT][hapmap]
rs7641764	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7646505	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7649682	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7651175	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs903518	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9812300	0.85[JPT][hapmap]
rs9814419	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9820931	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9825835	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9835256	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9839409	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9841308	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9841518	0.84[ASN][1000 genomes]
rs9844723	0.85[ASN][1000 genomes]
rs9845536	0.82[ASN][1000 genomes]
rs9881808	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9882514	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][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	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1004417	chr3:23318797-23389422	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23350600-23366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:23355200-23365400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:23355800-23366000	Weak transcription	Ovary	ovary
4	chr3:23356800-23365400	Weak transcription	Brain Anterior Caudate	brain
5	chr3:23356800-23367600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:23357000-23378800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:23357600-23366600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:23357800-23366000	Weak transcription	HSMM	muscle
9	chr3:23358400-23366400	Weak transcription	HSMMtube	muscle
10	chr3:23359200-23366000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr3:23361600-23365200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:23361600-23365800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:23361600-23366400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:23362600-23363200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:23362600-23363800	Enhancers	Brain Hippocampus Middle	brain
16	chr3:23362800-23363200	Enhancers	Esophagus	oesophagus
17	chr3:23362800-23363200	Enhancers	Left Ventricle	heart
18	chr3:23362800-23363200	Enhancers	Right Ventricle	heart
19	chr3:23362800-23366000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:23363000-23363200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:23363000-23363200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr3:23363000-23366400	Weak transcription	Brain Inferior Temporal Lobe	brain

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