Variant report

Variant	rs7790650
Chromosome Location	chr7:78786971-78786972
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10245876	0.81[ASN][1000 genomes]
rs10255710	0.84[GIH][hapmap]
rs10255742	0.95[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.90[ASN][1000 genomes]
rs10280055	0.82[GIH][hapmap]
rs10953780	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs10953783	0.85[CEU][hapmap];0.93[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs11760355	0.82[CEU][hapmap];0.98[GIH][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes]
rs11767464	0.80[GIH][hapmap]
rs11982713	0.88[EUR][1000 genomes]
rs12112164	0.94[CEU][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12534678	0.92[EUR][1000 genomes]
rs12668450	0.89[CEU][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap]
rs12706023	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs13222189	0.81[CHB][hapmap];0.93[EUR][1000 genomes]
rs13222396	0.93[EUR][1000 genomes]
rs13239380	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs13309906	0.86[EUR][1000 genomes]
rs1468660	0.94[CEU][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs1990432	0.84[CEU][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes]
rs1990433	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024254	0.89[CEU][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.90[MEX][hapmap]
rs2191807	0.91[EUR][1000 genomes]
rs2191808	0.94[CEU][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2215584	0.93[EUR][1000 genomes]
rs2215585	0.80[GIH][hapmap]
rs2302441	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs2302442	0.91[EUR][1000 genomes]
rs34707261	0.93[EUR][1000 genomes]
rs4020771	0.89[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs4573181	0.85[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs4727816	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs4730678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730688	0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]
rs6466519	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6466533	0.85[CEU][hapmap];0.93[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs6466535	0.89[CEU][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap]
rs6950691	0.89[CEU][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap]
rs6957950	0.94[CEU][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6967793	0.84[CEU][hapmap]
rs6971099	0.89[GIH][hapmap]
rs7787597	0.89[CEU][hapmap];1.00[GIH][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs7788638	0.87[EUR][1000 genomes]
rs7789660	0.94[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7791658	0.85[CEU][hapmap]
rs7793860	0.89[CEU][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap]
rs7801546	0.92[EUR][1000 genomes]
rs983846	0.94[CEU][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.84[ASN][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	nsv831040	chr7:78623195-78831998	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv888510	chr7:78742376-78865618	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1033988	chr7:78778675-78851897	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv5806	chr7:78780156-78855716	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv888511	chr7:78784444-78851126	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1023323	chr7:78785484-78808172	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7790650	CD28	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78781800-78794400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr7:78786000-78794800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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