Variant report

Variant	rs17342342
Chromosome Location	chr3:23277035-23277036
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	chr3:23267196..23270682-chr3:23275861..23279079,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1027380	0.88[ASN][1000 genomes]
rs11711630	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715107	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13087416	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13095887	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1390083	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1495133	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1495134	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1552931	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2047340	0.82[AMR][1000 genomes]
rs2055155	0.81[ASN][1000 genomes]
rs2088129	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2132145	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2132147	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2132148	0.95[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2132149	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36073188	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4293660	0.83[ASN][1000 genomes]
rs4334589	0.98[ASN][1000 genomes]
rs4858065	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858066	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858488	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858498	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6769959	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6790185	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6799861	0.90[ASN][1000 genomes]
rs6806387	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73149661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618910	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7629327	0.87[ASN][1000 genomes]
rs7635882	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7636532	0.81[ASN][1000 genomes]
rs7648425	0.89[ASN][1000 genomes]
rs903519	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs923996	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9826103	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9836135	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9840015	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9844558	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9848331	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23261400-23278200	Weak transcription	Brain Angular Gyrus	brain
2	chr3:23265400-23282000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:23266200-23277800	Weak transcription	Fetal Thymus	thymus
4	chr3:23270600-23278200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:23270600-23278400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:23271200-23278200	Weak transcription	Right Ventricle	heart
7	chr3:23272600-23283000	Weak transcription	HMEC	breast
8	chr3:23273600-23277800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:23274400-23280800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:23274600-23278200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:23274600-23278200	Weak transcription	Left Ventricle	heart
12	chr3:23274600-23279800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:23274600-23281400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:23274600-23283000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:23274800-23277800	Weak transcription	Brain Substantia Nigra	brain
16	chr3:23274800-23278000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:23274800-23278000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:23274800-23278200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:23274800-23280200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:23274800-23298200	Weak transcription	Aorta	Aorta
21	chr3:23275000-23277800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:23275000-23278000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:23275000-23280800	Weak transcription	Brain Anterior Caudate	brain
24	chr3:23276400-23279600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:23276800-23277400	Enhancers	Psoas Muscle	Psoas
26	chr3:23276800-23281000	Weak transcription	Fetal Heart	heart
27	chr3:23277000-23277400	Enhancers	Ovary	ovary
28	chr3:23277000-23279600	Weak transcription	Brain Hippocampus Middle	brain

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