Variant report

Variant	rs10423874
Chromosome Location	chr19:19359500-19359501
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

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];0.87[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];0.91[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]
rs1064395	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];0.92[EUR][1000 genomes]
rs1557723	0.81[EUR][1000 genomes]
rs17216041	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17751061	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1989867	0.81[EUR][1000 genomes]
rs2010506	0.93[CEU][hapmap];0.94[EUR][1000 genomes]
rs2011503	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2060274	0.87[CEU][hapmap]
rs2060275	0.87[CEU][hapmap]
rs2074302	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2315023	0.90[EUR][1000 genomes]
rs2916070	0.87[CEU][hapmap]
rs2965184	0.87[CEU][hapmap]
rs2965186	0.85[CEU][hapmap]
rs2965195	0.87[CEU][hapmap]
rs2965201	0.87[CEU][hapmap]
rs35854118	0.94[EUR][1000 genomes]
rs3752150	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3752170	0.81[ASN][1000 genomes]
rs4239639	0.83[EUR][1000 genomes]
rs4563151	0.80[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4808932	1.00[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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	0.87[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];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	0.87[CEU][hapmap]
rs756999	0.81[EUR][1000 genomes]
rs8100097	0.82[EUR][1000 genomes]
rs8105642	0.87[CEU][hapmap]
rs8108777	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs998732	1.00[CEU][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10423874	SF4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19345800-19359600	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:19345800-19360400	Weak transcription	Brain Angular Gyrus	brain
3	chr19:19346000-19363200	Strong transcription	Fetal Brain Female	brain
4	chr19:19346000-19367000	Weak transcription	Brain Anterior Caudate	brain
5	chr19:19347400-19367200	Weak transcription	Fetal Brain Male	brain
6	chr19:19354800-19362400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:19354800-19363400	Strong transcription	Brain Germinal Matrix	brain
8	chr19:19357400-19363000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:19358800-19362000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:19359200-19361600	Strong transcription	Brain Cingulate Gyrus	brain
11	chr19:19359400-19359800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:19359400-19361200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:19359400-19361600	Strong transcription	Brain Inferior Temporal Lobe	brain

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