Variant report

Variant	rs6475641
Chromosome Location	chr9:22398466-22398467
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10121840	0.81[EUR][1000 genomes]
rs10491847	0.94[ASN][1000 genomes]
rs12005191	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13289310	0.81[EUR][1000 genomes]
rs1410976	0.83[EUR][1000 genomes]
rs1410980	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1576333	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17835236	0.81[EUR][1000 genomes]
rs1887968	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28819371	0.87[EUR][1000 genomes]
rs2891170	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4977581	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs596543	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6415739	0.95[EUR][1000 genomes]
rs7024068	0.80[EUR][1000 genomes]
rs7047581	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7846900	0.85[EUR][1000 genomes]
rs7854056	0.95[EUR][1000 genomes]
rs7863670	0.81[EUR][1000 genomes]
rs7864281	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7870644	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7875648	0.80[EUR][1000 genomes]
rs9696718	0.90[EUR][1000 genomes]

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	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016067	chr9:22210874-22432654	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1015364	chr9:22211364-22416886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv540086	chr9:22211364-22416886	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1023972	chr9:22246764-22426267	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv540087	chr9:22246764-22426267	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1031822	chr9:22364573-22490686	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv869121	chr9:22382290-23232146	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv892750	chr9:22383816-22496640	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6475641	DMRTA1	cis	parietal	SCAN
rs6475641	IFNA21	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22397000-22399200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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