Variant report

Variant	rs476924
Chromosome Location	chr9:22431172-22431173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10115557	0.83[ASN][1000 genomes]
rs10121840	0.85[ASN][1000 genomes]
rs12005191	0.85[ASN][1000 genomes]
rs13289310	0.85[ASN][1000 genomes]
rs1329396	1.00[JPT][hapmap]
rs17835236	0.82[ASN][1000 genomes]
rs1887967	0.83[ASN][1000 genomes]
rs2671621	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4977778	0.85[ASN][1000 genomes]
rs526139	0.96[CEU][hapmap]
rs527772	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs535729	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs536649	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs566993	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs596543	0.96[CEU][hapmap];0.96[YRI][hapmap]
rs603582	1.00[ASN][1000 genomes]
rs640693	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs659815	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs659842	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs664198	0.92[EUR][1000 genomes]
rs679066	0.82[ASN][1000 genomes]
rs7024068	0.83[ASN][1000 genomes]
rs7033177	0.85[ASN][1000 genomes]
rs7846900	0.83[ASN][1000 genomes]
rs7847145	0.83[ASN][1000 genomes]
rs7870619	0.85[ASN][1000 genomes]
rs7875648	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
6	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
7	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
8	esv2761508	chr9:22400968-22819938	Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1016983	chr9:22412948-22672062	Bivalent/Poised TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1027227	chr9:22416348-22666768	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv540088	chr9:22416348-22666768	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv533941	chr9:22416549-23232146	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs476924	DMRTA1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22426000-22434600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:22429200-22431200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:22429200-22431400	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr9:22429400-22432400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr9:22430000-22431200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr9:22431000-22432000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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