Variant report

Variant	rs1859485
Chromosome Location	chr7:71597668-71597669
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10216301	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10239345	1.00[ASN][1000 genomes]
rs10243592	1.00[ASN][1000 genomes]
rs10243727	1.00[ASN][1000 genomes]
rs10247132	1.00[ASN][1000 genomes]
rs10250790	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10258574	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10267684	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10274382	1.00[ASN][1000 genomes]
rs10281483	1.00[ASN][1000 genomes]
rs10950299	1.00[ASN][1000 genomes]
rs10950300	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10950302	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11772518	1.00[CHB][hapmap]
rs11981190	0.85[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs1232514	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12533623	1.00[CHB][hapmap]
rs12699125	0.83[ASW][hapmap];0.81[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13230379	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13231782	0.89[ASN][1000 genomes]
rs1474389	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17605262	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17673882	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17673922	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1859484	0.94[ASN][1000 genomes]
rs1996399	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2158562	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2189846	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2214663	0.88[ASN][1000 genomes]
rs2677284	0.80[EUR][1000 genomes]
rs28447164	0.82[ASN][1000 genomes]
rs2867603	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2867605	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34829642	1.00[ASN][1000 genomes]
rs4577845	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4717627	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4717631	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4719218	1.00[ASN][1000 genomes]
rs548613	1.00[JPT][hapmap]
rs6953054	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6954622	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6957682	0.88[ASN][1000 genomes]
rs6972469	1.00[ASN][1000 genomes]
rs6974563	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977679	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7778610	0.81[ASN][1000 genomes]
rs7786666	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7787176	1.00[ASN][1000 genomes]
rs7795273	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7803192	1.00[CHB][hapmap]
rs7805893	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7808523	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs844719	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs844762	1.00[CHB][hapmap]
rs844767	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs860002	0.88[ASN][1000 genomes]
rs860003	0.88[ASN][1000 genomes]
rs860007	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs860008	0.88[ASN][1000 genomes]
rs860010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs860012	0.81[ASN][1000 genomes]
rs860013	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs860014	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs861491	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs865225	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs875499	1.00[JPT][hapmap]
rs917211	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9647948	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026896	chr7:71003462-71721516	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv916220	chr7:71200006-71708048	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv531372	chr7:71300090-71909517	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv491610	chr7:71422560-71803630	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv531373	chr7:71487076-71765613	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv817506	chr7:71488542-71935721	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv1034282	chr7:71531113-71876617	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1015848	chr7:71552185-71736068	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv538942	chr7:71552185-71736068	ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv831024	chr7:71569349-71735250	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1023496	chr7:71593461-71633053	Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1859485	GTF2IRD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:71588200-71603800	Weak transcription	Thymus	Thymus
2	chr7:71596800-71598800	Weak transcription	Fetal Thymus	thymus

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