Variant report

Variant	rs7012516
Chromosome Location	chr8:50118527-50118528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10092709	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10097641	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1021036	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10504077	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10808750	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10957383	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10957385	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11777050	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11986211	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11994922	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11998708	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13263230	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1383272	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1613684	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1617791	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1842400	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1876720	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2175033	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2219896	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385328	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2385330	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2385331	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2726710	0.91[JPT][hapmap]
rs2726711	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2726714	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35395861	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35655170	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4256605	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4461912	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4501593	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4873325	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4873347	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4873348	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4873349	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55987135	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62508747	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6472291	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6982179	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6988643	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6999524	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7006071	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71548493	0.91[AFR][1000 genomes]
rs7817650	0.81[AMR][1000 genomes]
rs7818564	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7824009	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7828104	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7833419	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7836969	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7840704	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7841358	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7844505	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7845374	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025068	chr8:49953397-50370208	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1034908	chr8:50023423-50416049	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv539601	chr8:50023423-50416049	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1024410	chr8:50037085-50511501	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv428517	chr8:50094920-50232993	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv890855	chr8:50109365-50252962	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv819662	chr8:50115746-50122871	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7012516	SNTG1	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:50118200-50118600	Enhancers	GM12878-XiMat	blood
2	chr8:50118400-50119400	Enhancers	Stomach Mucosa	stomach
3	chr8:50118400-50122200	Weak transcription	Pancreas	Pancrea

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