Variant report

Variant	rs1452769
Chromosome Location	chr2:50396135-50396136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10490240	0.91[CEU][hapmap]
rs11125289	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11125290	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11125291	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11125292	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11125294	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11125295	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs11125296	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11888330	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs11896556	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs11900502	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12466807	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12468151	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12468252	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12468282	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12468342	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12468396	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12468477	1.00[CEU][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs12470518	0.85[CHB][hapmap]
rs12475100	0.86[CEU][hapmap];0.95[CHB][hapmap]
rs12476530	0.84[CHB][hapmap]
rs12478603	0.84[CHB][hapmap];0.83[ASN][1000 genomes]
rs12613266	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12613363	0.89[CHB][hapmap]
rs12622844	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1377238	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs1421573	0.92[CEU][hapmap];0.90[CHB][hapmap]
rs1452770	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1452771	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1452773	0.84[CHB][hapmap]
rs1517827	0.86[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs1563019	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs1563020	0.86[CEU][hapmap]
rs1563028	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs1584763	1.00[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17039764	0.90[CHB][hapmap]
rs17039900	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17039905	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17039932	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs17039940	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs17039947	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17039976	1.00[CEU][hapmap];0.80[CHB][hapmap]
rs17039979	1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs17039985	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17040013	1.00[CEU][hapmap]
rs17040034	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs17040064	0.86[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17040090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17040117	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap]
rs17040123	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs17040138	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17040141	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17040147	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17040160	0.82[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17040169	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17040210	0.87[MEX][hapmap]
rs2176872	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2218979	0.89[CHB][hapmap]
rs4971649	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4971650	1.00[CEU][hapmap]
rs4971652	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971653	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4971654	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4971655	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs4971656	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap]
rs4971658	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971659	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971661	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60500567	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545149	0.90[CHB][hapmap]
rs6545155	0.85[CHB][hapmap]
rs6712102	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs6712119	0.92[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap]
rs6712423	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs6731397	0.86[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72878157	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72881242	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7599349	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs7607863	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv934303	chr2:50145598-50412189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv932915	chr2:50306630-50628415	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2756107	chr2:50307245-50440043	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948833	chr2:50307245-50459077	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1002344	chr2:50326207-50518933	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv535692	chr2:50326207-50518933	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1452769	ATP6V1E2	cis	parietal	SCAN
rs1452769	CRIPT	cis	cerebellum	SCAN
rs1452769	PRKCE	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50395800-50396800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr2:50396000-50396400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:50396000-50396400	Enhancers	Brain Germinal Matrix	brain

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