Variant report

Variant	rs12670442
Chromosome Location	chr7:78927445-78927446
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:78926978..78927922-chr7:79676854..79677685,3	MCF-7	breast:
2	chr7:78927254..78927762-chr7:79370740..79371579,2	MCF-7	breast:
3	chr7:78927198..78927954-chr7:79647855..79648713,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNAI1-7	chr7:78926788-78930237	ucscGeneNc_uc010lea_1

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10085854	0.86[EUR][1000 genomes]
rs10225318	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10244816	1.00[EUR][1000 genomes]
rs10247922	1.00[JPT][hapmap]
rs10248439	1.00[JPT][hapmap]
rs10248584	1.00[JPT][hapmap]
rs10258290	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10261439	1.00[JPT][hapmap]
rs10263112	1.00[JPT][hapmap]
rs10264341	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10274797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10276665	1.00[JPT][hapmap]
rs10485936	1.00[JPT][hapmap]
rs1100310	1.00[JPT][hapmap]
rs1155234	1.00[JPT][hapmap]
rs11972217	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs11974844	0.90[EUR][1000 genomes]
rs11974872	0.90[EUR][1000 genomes]
rs11977156	1.00[EUR][1000 genomes]
rs11979157	0.90[EUR][1000 genomes]
rs11980152	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs11980253	1.00[JPT][hapmap]
rs12666679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12666680	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670971	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12670981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12706107	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358471	1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1406153	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]
rs1406154	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]
rs1406155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1406156	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1528262	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs1534492	1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1534493	1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1609273	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1609274	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1609275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1609276	1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16886435	1.00[JPT][hapmap]
rs16886457	1.00[JPT][hapmap]
rs16886476	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs16886549	1.00[JPT][hapmap]
rs17147873	1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs17152006	1.00[JPT][hapmap]
rs17152009	1.00[JPT][hapmap]
rs17152011	1.00[JPT][hapmap]
rs17152041	1.00[JPT][hapmap]
rs17152051	1.00[JPT][hapmap]
rs17152063	1.00[JPT][hapmap]
rs17152076	1.00[JPT][hapmap]
rs17152125	1.00[JPT][hapmap]
rs17152224	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs17152238	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs17152245	1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs17478565	1.00[JPT][hapmap]
rs17481134	1.00[JPT][hapmap]
rs17488042	1.00[JPT][hapmap]
rs17818755	1.00[JPT][hapmap]
rs1918930	1.00[JPT][hapmap]
rs1918932	1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1918933	0.85[EUR][1000 genomes]
rs1997277	0.90[EUR][1000 genomes]
rs2178169	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2364908	1.00[JPT][hapmap]
rs28401690	1.00[EUR][1000 genomes]
rs28450541	0.90[EUR][1000 genomes]
rs28611031	0.90[EUR][1000 genomes]
rs28700941	0.90[EUR][1000 genomes]
rs3919522	1.00[JPT][hapmap]
rs4727839	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]
rs4727840	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4727842	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4730753	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4730754	0.85[AFR][1000 genomes]
rs4730757	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56829360	0.90[EUR][1000 genomes]
rs59620956	1.00[EUR][1000 genomes]
rs61075638	0.90[EUR][1000 genomes]
rs6466602	0.90[EUR][1000 genomes]
rs6466622	1.00[JPT][hapmap]
rs6466638	1.00[JPT][hapmap]
rs6963053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963068	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]
rs6975958	1.00[EUR][1000 genomes]
rs73375128	1.00[EUR][1000 genomes]
rs73375139	1.00[EUR][1000 genomes]
rs73375150	1.00[EUR][1000 genomes]
rs73375151	1.00[EUR][1000 genomes]
rs73375156	1.00[EUR][1000 genomes]
rs73375167	0.90[EUR][1000 genomes]
rs7787904	1.00[JPT][hapmap]
rs7787956	1.00[JPT][hapmap]
rs7800314	1.00[JPT][hapmap]
rs7811441	1.00[JPT][hapmap]
rs848913	1.00[JPT][hapmap]
rs848932	1.00[JPT][hapmap]
rs848934	1.00[JPT][hapmap]
rs848948	1.00[JPT][hapmap]
rs848953	1.00[JPT][hapmap]
rs991261	1.00[JPT][hapmap]

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:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78922400-78929200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr7:78923200-78930000	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:78924000-78930600	Weak transcription	A549	lung
4	chr7:78927200-78932400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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