Variant report

Variant	rs1064395
Chromosome Location	chr19:19361735-19361736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19359798..19362582-chr19:19364132..19366606,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10401714	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403273	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10407933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417330	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10422893	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10423659	0.81[ASN][1000 genomes]
rs10423874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11555053	1.00[CEU][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs1557723	0.81[EUR][1000 genomes]
rs17216041	1.00[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17751061	0.93[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs1989867	0.81[EUR][1000 genomes]
rs2010506	0.93[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs2011503	0.81[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs2060274	0.81[CEU][hapmap]
rs2060275	0.81[CEU][hapmap]
rs2074302	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2315023	0.90[EUR][1000 genomes]
rs2916070	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs2965184	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs2965186	0.96[TSI][hapmap]
rs2965190	0.90[TSI][hapmap]
rs2965195	0.81[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2965201	0.81[CEU][hapmap];0.96[TSI][hapmap]
rs35854118	0.94[EUR][1000 genomes]
rs3752150	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs3752170	0.81[ASN][1000 genomes]
rs4239639	0.83[EUR][1000 genomes]
rs4563151	0.80[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4808932	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808933	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808934	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4808944	0.90[EUR][1000 genomes]
rs4808951	0.81[CEU][hapmap]
rs55762233	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55765017	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55822665	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56044734	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56135441	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56144632	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56212061	0.84[EUR][1000 genomes]
rs56278919	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57436187	0.88[EUR][1000 genomes]
rs6511027	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7257875	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72999030	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72999059	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72999063	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72999068	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs756997	0.81[CEU][hapmap]
rs756999	0.81[EUR][1000 genomes]
rs8100097	0.82[EUR][1000 genomes]
rs8105642	0.81[CEU][hapmap]
rs8108777	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8110171	0.81[CEU][hapmap]
rs8110250	0.81[CEU][hapmap]
rs998732	1.00[CEU][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bipolar disorder	21353194	GWAS catalog

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1064395	LOC440518	cis	parietal	SCAN
rs1064395	DDX49	cis	cerebellum	SCAN
rs1064395	GATAD2A	cis	parietal	SCAN
rs1064395	LSM4	cis	cerebellum	SCAN
rs1064395	OCEL1	cis	parietal	SCAN
rs1064395	IL12RB1	cis	parietal	SCAN
rs1064395	EDG4	cis	multi-tissue	Pritchard
rs1064395	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19346000-19363200	Strong transcription	Fetal Brain Female	brain
2	chr19:19346000-19367000	Weak transcription	Brain Anterior Caudate	brain
3	chr19:19347400-19367200	Weak transcription	Fetal Brain Male	brain
4	chr19:19354800-19362400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr19:19354800-19363400	Strong transcription	Brain Germinal Matrix	brain
6	chr19:19357400-19363000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:19358800-19362000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:19361000-19362600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:19361400-19366600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:19361600-19367400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:19361600-19367800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr19:19361600-19372200	Weak transcription	Brain Angular Gyrus	brain

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