Variant report

Variant	rs2946580
Chromosome Location	chr7:65531842-65531843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10950024	0.80[ASN][1000 genomes]
rs10950025	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10950027	0.83[AMR][1000 genomes]
rs10950029	0.83[AMR][1000 genomes]
rs11760805	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12666485	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12673308	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs160636	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs160641	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs160645	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs160647	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451953	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2460427	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2465121	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs313818	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs313823	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs313828	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs313830	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs313834	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs316305	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs316306	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs316316	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs316320	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs316323	0.80[ASN][1000 genomes]
rs316324	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs316328	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs316336	0.83[EUR][1000 genomes]
rs400767	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4441996	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4718301	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6460276	0.83[AMR][1000 genomes]
rs67302640	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs67397473	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs67688847	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6960870	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs73136346	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs73376401	0.83[AMR][1000 genomes]
rs7787063	0.86[AMR][1000 genomes];0.82[ASN][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	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv888325	chr7:65474919-65575893	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1021186	chr7:65492601-65663438	Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv984546	chr7:65531382-65556631	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2946580	GTF2IRD1P1	cis	Thyroid	GTEx
rs2946580	GS1-124K5.4	cis	Stomach	GTEx
rs2946580	GS1-124K5.11	cis	Thyroid	GTEx
rs2946580	RNU6-96P	cis	Thyroid	GTEx
rs2946580	GS1-124K5.4	cis	Artery Aorta	GTEx
rs2946580	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs2946580	RP4-756H11.3	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65531200-65537600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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