Variant report

Variant	rs17056425
Chromosome Location	chr9:73794362-73794363
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10868991	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868997	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11142711	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142717	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142719	1.00[ASN][1000 genomes]
rs11142736	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142750	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142753	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11142757	1.00[ASN][1000 genomes]
rs11142763	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142773	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142774	0.84[EUR][1000 genomes]
rs11142777	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142778	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142779	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142780	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11142781	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005021	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12378604	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12379392	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12380581	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504388	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504389	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504390	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504391	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504392	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1504404	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532801	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532802	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1532804	0.89[EUR][1000 genomes]
rs17056483	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17616798	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2174308	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309916	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309917	0.83[EUR][1000 genomes]
rs2871376	0.83[EUR][1000 genomes]
rs35533028	1.00[ASN][1000 genomes]
rs4079469	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370599	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4370600	1.00[ASN][1000 genomes]
rs7018911	0.85[EUR][1000 genomes]
rs7021834	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027219	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7039341	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040929	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7043726	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73467746	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73469317	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73469327	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73647995	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763359	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848661	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854181	0.89[EUR][1000 genomes]
rs7854330	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870153	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9785216	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9785312	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs985654	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv1035505	chr9:73709852-73934353	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv893442	chr9:73778502-74115344	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv984559	chr9:73789685-73831841	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
4	nsv1052375	chr9:73793681-73893133	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv540152	chr9:73793681-73893133	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17056425	TRPM3	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73794000-73794400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:73794000-73794400	Active TSS	Brain Anterior Caudate	brain
3	chr9:73794000-73794600	Enhancers	Fetal Intestine Small	intestine
4	chr9:73794200-73794600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr9:73794200-73797800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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