Variant report

Variant	rs16886524
Chromosome Location	chr7:78937050-78937051
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	chr7:78936738..78938800-chr7:78940617..78942122,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1015639	0.85[CHB][hapmap]
rs10237509	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs10274885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10280554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10485955	0.89[ASW][hapmap];0.92[CHD][hapmap]
rs1071038	1.00[CEU][hapmap];0.92[CHB][hapmap]
rs10808182	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10953834	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953851	0.85[MEX][hapmap]
rs11773085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12706097	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1358472	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1406165	0.86[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs1406166	0.81[EUR][1000 genomes]
rs1528259	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1528260	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1528264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1528268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1528276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1528282	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1609281	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16886545	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16886548	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17152178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17152192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17152223	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17152382	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17237664	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap]
rs1881293	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1881294	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1881298	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1881299	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes]
rs1918935	0.89[ASW][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap]
rs2190174	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2364913	0.93[MEX][hapmap]
rs41364851	0.89[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap]
rs6944731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6954793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6964349	0.85[CHB][hapmap]
rs6966599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6966753	0.85[CHB][hapmap]
rs6974095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73153203	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154930	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154978	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156041	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73156043	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73156068	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73156084	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7778707	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7806210	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7808561	0.86[MEX][hapmap]
rs7811833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs984708	1.00[MEX][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16886524	MAGI2	cis	cerebellum	SCAN
rs16886524	TMEM120A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78934200-78937600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:78935800-78937600	Enhancers	A549	lung
3	chr7:78936400-78937200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:78936400-78938000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr7:78937000-78937200	Enhancers	Liver	Liver

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