Variant report

Variant	rs984708
Chromosome Location	chr7:79025106-79025107
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	chr7:79017286..79019685-chr7:79023052..79025297,2	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1015639	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10244234	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10254950	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10262441	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10272027	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10280554	0.85[CEU][hapmap]
rs10281359	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10452985	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10485955	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10953834	0.82[EUR][1000 genomes]
rs10953851	0.92[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10953852	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10953862	0.85[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap]
rs11773085	0.93[MEX][hapmap]
rs11976606	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11983573	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530628	0.84[ASN][1000 genomes]
rs12672249	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1406165	0.92[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1406166	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1528259	0.92[CEU][hapmap];0.97[EUR][1000 genomes]
rs1528260	0.92[CEU][hapmap];0.97[EUR][1000 genomes]
rs1528264	0.85[EUR][1000 genomes]
rs1528276	0.84[EUR][1000 genomes]
rs1528278	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1528279	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1528282	0.97[EUR][1000 genomes]
rs16886524	1.00[MEX][hapmap]
rs16886545	0.97[EUR][1000 genomes]
rs16886548	0.97[EUR][1000 genomes]
rs17152382	0.96[EUR][1000 genomes]
rs17421243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1859599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1881293	0.86[EUR][1000 genomes]
rs1881299	0.86[MEX][hapmap]
rs1918935	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2158708	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2190174	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs2190175	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2364913	1.00[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2364918	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28396540	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28459297	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28691838	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34599162	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35763479	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41364851	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4141207	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4141208	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4562253	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4730828	0.85[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap]
rs4730829	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4730831	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs55637636	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55713683	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58310347	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6466621	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6466649	1.00[JPT][hapmap]
rs66499867	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66775453	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66778115	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66900251	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66961385	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67092648	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67122557	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67289031	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67486505	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67685126	0.98[EUR][1000 genomes]
rs68113978	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6947186	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6949538	0.83[JPT][hapmap]
rs6954793	0.93[MEX][hapmap]
rs6964030	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6964349	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6966599	1.00[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs6966753	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs727391	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73141612	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73156041	0.97[EUR][1000 genomes]
rs73156043	0.97[EUR][1000 genomes]
rs73156068	0.96[EUR][1000 genomes]
rs73156084	0.97[EUR][1000 genomes]
rs73157803	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157805	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157824	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157844	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73157878	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73381312	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7455557	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7778707	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs7785706	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7788509	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7792796	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7795832	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7799230	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7803773	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7806210	0.97[EUR][1000 genomes]
rs7807048	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7808561	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7811833	1.00[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs970491	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9918566	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs993860	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9969308	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9969320	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
5	nsv464600	chr7:78981719-79030922	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv607663	chr7:78981719-79030922	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv888514	chr7:78987060-79061837	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv888515	chr7:78987060-79221707	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv607664	chr7:78998409-79057761	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs984708	MAGI2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79017600-79030400	Weak transcription	Brain Substantia Nigra	brain
2	chr7:79023200-79025800	Weak transcription	Gastric	stomach
3	chr7:79023800-79027400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:79024000-79025400	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:79024600-79026800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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