Variant report

Variant	rs28450541
Chromosome Location	chr7:78956546-78956547
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:28170954..28172471-chr7:78954883..78956578,2	MCF-7	breast:

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10085854	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225318	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10244816	0.90[EUR][1000 genomes]
rs10247922	0.80[ASN][1000 genomes]
rs10248439	0.80[ASN][1000 genomes]
rs10258290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10260696	0.80[ASN][1000 genomes]
rs10261439	0.80[ASN][1000 genomes]
rs10263112	0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10264341	0.90[EUR][1000 genomes]
rs10269542	0.80[ASN][1000 genomes]
rs10274797	0.90[EUR][1000 genomes]
rs10275975	0.80[ASN][1000 genomes]
rs10276665	0.80[ASN][1000 genomes]
rs11972217	0.81[EUR][1000 genomes]
rs11974844	0.81[EUR][1000 genomes]
rs11974872	0.81[EUR][1000 genomes]
rs11977156	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11979157	0.81[EUR][1000 genomes]
rs11980152	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12666679	0.82[EUR][1000 genomes]
rs12666680	0.90[EUR][1000 genomes]
rs12670442	0.90[EUR][1000 genomes]
rs12670971	0.86[EUR][1000 genomes]
rs12670981	0.90[EUR][1000 genomes]
rs12706106	0.90[EUR][1000 genomes]
rs12706107	0.90[EUR][1000 genomes]
rs1358471	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1406153	0.90[EUR][1000 genomes]
rs1406154	0.90[EUR][1000 genomes]
rs1406155	0.90[EUR][1000 genomes]
rs1406156	0.90[EUR][1000 genomes]
rs1528262	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534492	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1534493	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1609273	0.90[EUR][1000 genomes]
rs1609274	0.90[EUR][1000 genomes]
rs1609275	0.90[EUR][1000 genomes]
rs1609276	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16886476	0.81[EUR][1000 genomes]
rs16886549	0.80[ASN][1000 genomes]
rs17147873	0.81[EUR][1000 genomes]
rs17152224	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17152238	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17152245	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17421940	0.80[ASN][1000 genomes]
rs17478565	0.80[ASN][1000 genomes]
rs17481134	0.80[ASN][1000 genomes]
rs17818755	0.80[ASN][1000 genomes]
rs1918930	0.80[ASN][1000 genomes]
rs1918932	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1997277	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178169	0.90[EUR][1000 genomes]
rs2364908	0.80[ASN][1000 genomes]
rs28401690	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28611031	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700941	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727839	0.90[EUR][1000 genomes]
rs4727840	0.90[EUR][1000 genomes]
rs4727842	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4730757	0.90[EUR][1000 genomes]
rs4730758	0.90[EUR][1000 genomes]
rs56829360	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59620956	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61075638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62458985	0.80[ASN][1000 genomes]
rs62458986	0.80[ASN][1000 genomes]
rs62458987	0.80[ASN][1000 genomes]
rs62458988	0.80[ASN][1000 genomes]
rs62458989	0.80[ASN][1000 genomes]
rs62458990	0.80[ASN][1000 genomes]
rs6466602	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466622	0.80[ASN][1000 genomes]
rs6466638	0.80[ASN][1000 genomes]
rs6963053	0.90[EUR][1000 genomes]
rs6963068	0.90[EUR][1000 genomes]
rs6975958	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6977556	0.80[ASN][1000 genomes]
rs73375128	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73375139	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73375150	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73375151	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73375156	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73375167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787904	0.85[ASN][1000 genomes]
rs7787956	0.80[ASN][1000 genomes]
rs7800314	0.80[ASN][1000 genomes]
rs7811441	0.80[ASN][1000 genomes]
rs848916	0.80[ASN][1000 genomes]
rs848932	0.80[ASN][1000 genomes]
rs848934	0.80[ASN][1000 genomes]
rs848944	0.80[ASN][1000 genomes]
rs848948	0.80[ASN][1000 genomes]
rs848953	0.80[ASN][1000 genomes]
rs991261	0.80[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	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1029799	chr7:78608097-79061737	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv831041	chr7:78819499-78973222	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2764028	chr7:78874740-79112630	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78947400-78956600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:78955400-78958800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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