Variant report

Variant	rs7778707
Chromosome Location	chr7:78980026-78980027
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1015639	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10237509	0.86[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap]
rs10244234	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10254950	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10262441	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10272027	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs10274885	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs10280554	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10281359	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10452985	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10485955	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1071038	0.86[CEU][hapmap];0.92[CHB][hapmap]
rs10953834	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10953851	0.85[CEU][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs10953852	0.85[EUR][1000 genomes]
rs11773085	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[MEX][hapmap]
rs11976606	0.89[EUR][1000 genomes]
rs11983573	0.95[EUR][1000 genomes]
rs12672249	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs12706097	0.86[CEU][hapmap];0.92[CHB][hapmap]
rs1358472	0.86[CEU][hapmap]
rs1406165	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1406166	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1528259	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1528260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1528264	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1528268	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs1528276	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1528278	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1528279	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1528282	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16886524	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]
rs16886545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16886548	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17152178	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs17152192	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs17152223	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17152382	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17237664	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs17421243	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1859599	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1881293	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1881294	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1881299	0.86[CEU][hapmap];0.81[CHB][hapmap];0.86[MEX][hapmap]
rs1918935	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2158708	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2190174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2190175	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs2364913	0.92[CEU][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs2364918	0.90[EUR][1000 genomes]
rs28396540	0.82[EUR][1000 genomes]
rs28459297	0.82[EUR][1000 genomes]
rs28691838	0.82[EUR][1000 genomes]
rs34599162	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35763479	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41364851	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4141207	0.89[EUR][1000 genomes]
rs4141208	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4562253	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55637636	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55713683	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58310347	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6466621	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs66499867	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66775453	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66778115	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66900251	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs66961385	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67092648	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67122557	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67289031	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67486505	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67685126	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68113978	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6944731	0.86[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs6947186	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6954793	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[MEX][hapmap]
rs6964030	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6964349	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6966599	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6966753	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6974095	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs727391	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs73141612	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73154978	0.80[EUR][1000 genomes]
rs73156041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73156043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73156068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73156084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73157803	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73157805	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73157824	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73157844	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73157878	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73381312	0.85[EUR][1000 genomes]
rs7455557	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7785706	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs7788509	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7792796	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7795832	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7799230	0.89[EUR][1000 genomes]
rs7803773	0.88[EUR][1000 genomes]
rs7806210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7807048	0.85[EUR][1000 genomes]
rs7808561	0.92[CEU][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs7811833	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs970491	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs984708	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs9918566	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs993860	0.82[EUR][1000 genomes]
rs9969308	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs9969320	0.82[EUR][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	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	esv2762681	chr7:78958864-78982993	Enhancers Active TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7778707	LOC402560	cis	multi-tissue	Pritchard
rs7778707	MAGI2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78971800-78981800	Weak transcription	Brain Angular Gyrus	brain
2	chr7:78977200-78981800	Weak transcription	Fetal Heart	heart
3	chr7:78979600-78981000	Weak transcription	Brain Hippocampus Middle	brain
4	chr7:78979600-78981600	Weak transcription	Ovary	ovary
5	chr7:78979800-78980200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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