Variant report

Variant	rs28601738
Chromosome Location	chr7:79704607-79704608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1012825	0.90[ASN][1000 genomes]
rs10227476	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10228945	0.86[EUR][1000 genomes]
rs10239028	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10250102	0.86[EUR][1000 genomes]
rs10250164	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10268369	0.87[EUR][1000 genomes]
rs10270142	0.83[ASN][1000 genomes]
rs10271308	0.86[EUR][1000 genomes]
rs10275775	0.87[EUR][1000 genomes]
rs1034699	0.92[ASN][1000 genomes]
rs1034701	0.92[ASN][1000 genomes]
rs1034722	0.88[EUR][1000 genomes]
rs10486922	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1074944	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10954036	0.86[ASN][1000 genomes]
rs11769881	0.83[ASN][1000 genomes]
rs11770145	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11975430	0.90[ASN][1000 genomes]
rs12154241	0.85[ASN][1000 genomes]
rs12154320	0.85[ASN][1000 genomes]
rs1319268	0.86[EUR][1000 genomes]
rs13437829	0.92[ASN][1000 genomes]
rs17803489	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17804483	0.90[ASN][1000 genomes]
rs2007845	0.90[EUR][1000 genomes]
rs2012262	0.91[ASN][1000 genomes]
rs2189450	0.87[EUR][1000 genomes]
rs28588381	0.85[ASN][1000 genomes]
rs28609969	0.92[ASN][1000 genomes]
rs28698330	0.92[ASN][1000 genomes]
rs4727990	0.86[EUR][1000 genomes]
rs4727999	0.86[ASN][1000 genomes]
rs4731190	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4731202	0.85[ASN][1000 genomes]
rs58785310	0.88[ASN][1000 genomes]
rs61086456	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6466904	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6466916	0.85[ASN][1000 genomes]
rs6466926	0.91[EUR][1000 genomes]
rs6466928	0.87[EUR][1000 genomes]
rs67486586	0.92[ASN][1000 genomes]
rs6945977	0.88[ASN][1000 genomes]
rs6954322	0.87[EUR][1000 genomes]
rs6963566	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6966238	0.90[ASN][1000 genomes]
rs6966542	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6973019	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6975657	0.85[EUR][1000 genomes]
rs7778622	0.86[ASN][1000 genomes]
rs7778809	0.88[EUR][1000 genomes]
rs7783336	0.92[ASN][1000 genomes]
rs7792173	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799402	0.92[ASN][1000 genomes]
rs7799547	0.92[EUR][1000 genomes]
rs7805603	0.88[EUR][1000 genomes]
rs9655843	0.85[ASN][1000 genomes]
rs970112	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs970113	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429785	chr7:79589749-80177049	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv607678	chr7:79665817-79726578	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1027494	chr7:79693976-79760332	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28601738	GNAI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:79695800-79707400	Weak transcription	Psoas Muscle	Psoas
2	chr7:79696800-79707400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:79700800-79707400	Weak transcription	Adipose Nuclei	Adipose
4	chr7:79701200-79707400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:79704400-79704800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:79704400-79704800	Enhancers	Osteobl	bone
7	chr7:79704600-79704800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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