Variant report

Variant	rs10812228
Chromosome Location	chr9:25395935-25395936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10115498	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10115746	0.95[EUR][1000 genomes]
rs10119099	0.94[EUR][1000 genomes]
rs10119894	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10121903	0.94[EUR][1000 genomes]
rs10733401	0.94[EUR][1000 genomes]
rs10733402	0.94[EUR][1000 genomes]
rs10738716	0.95[EUR][1000 genomes]
rs10738717	0.94[EUR][1000 genomes]
rs10738718	0.94[EUR][1000 genomes]
rs10738719	0.94[EUR][1000 genomes]
rs10738720	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10757522	0.94[EUR][1000 genomes]
rs10757523	0.95[EUR][1000 genomes]
rs10757524	0.94[EUR][1000 genomes]
rs10757525	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757526	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757527	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757528	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757529	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757531	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757532	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757533	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757536	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10757538	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10757539	0.81[ASN][1000 genomes]
rs10812226	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10812229	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10812230	0.85[EUR][1000 genomes]
rs10812231	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10812233	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10812234	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10966883	0.93[EUR][1000 genomes]
rs10966884	0.95[EUR][1000 genomes]
rs10966885	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10966887	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10966893	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10966896	0.82[EUR][1000 genomes]
rs12377312	0.82[AFR][1000 genomes]
rs12685541	0.83[AFR][1000 genomes]
rs1327380	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1327381	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1327382	0.95[EUR][1000 genomes]
rs1327383	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1327394	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1576028	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1576029	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1576030	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1576040	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1590674	0.95[EUR][1000 genomes]
rs1616954	0.85[CEU][hapmap]
rs1668978	0.85[CEU][hapmap];0.88[GIH][hapmap];0.86[TSI][hapmap]
rs1831079	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1887377	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1901324	0.94[EUR][1000 genomes]
rs1901325	0.94[EUR][1000 genomes]
rs1901326	0.93[EUR][1000 genomes]
rs1901327	0.94[EUR][1000 genomes]
rs1901328	0.95[EUR][1000 genomes]
rs1998961	0.95[EUR][1000 genomes]
rs1998962	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2025826	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4083606	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4384070	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4449878	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4480194	0.95[EUR][1000 genomes]
rs57569675	0.83[ASN][1000 genomes]
rs7019841	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7019892	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7026882	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7040844	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7040859	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7041045	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7468705	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7850662	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7850668	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7850910	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7851064	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7855132	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7867884	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7868012	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7871092	0.86[AFR][1000 genomes]
rs943510	0.95[EUR][1000 genomes]
rs945811	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs980462	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033698	chr9:25109429-25410366	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv540099	chr9:25109429-25410366	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv466309	chr9:25157678-25683220	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv613889	chr9:25157678-25683220	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018570	chr9:25170659-25633419	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv540100	chr9:25170659-25633419	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv892816	chr9:25275811-25409024	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv892821	chr9:25283201-25409024	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv869035	chr9:25287213-25779281	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv892822	chr9:25295456-25396115	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv613908	chr9:25316440-25404108	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1033677	chr9:25325400-25583227	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv540101	chr9:25325400-25583227	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv531597	chr9:25325401-25779422	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv892824	chr9:25363830-25426760	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10812228	DMRTA1	cis	cerebellum	SCAN
rs10812228	C17orf37	trans	cerebellum	SCAN
rs10812228	C9orf82	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:25394000-25396200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:25394200-25396200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
3	chr9:25394200-25396600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
4	chr9:25394600-25399000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
5	chr9:25395000-25397400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:25395200-25396600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:25395400-25396400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
8	chr9:25395400-25398800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:25395600-25396000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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