Variant report

Variant	rs10882777
Chromosome Location	chr10:98119560-98119561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10736107	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10748673	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786277	0.84[CHD][hapmap]
rs10786281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10786282	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882773	0.84[CHD][hapmap]
rs10882778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882779	0.82[ASW][hapmap];0.90[CEU][hapmap];0.83[LWK][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10882781	0.90[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs10882783	0.82[JPT][hapmap]
rs11188734	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11188735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11188736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11818883	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11818896	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11818942	0.89[CHB][hapmap];0.83[CHD][hapmap]
rs1923707	0.84[CHD][hapmap]
rs2273891	0.84[CHD][hapmap]
rs2861572	1.00[JPT][hapmap]
rs2861575	0.92[YRI][hapmap];0.87[AFR][1000 genomes]
rs2861576	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789942	0.89[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs3814223	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818313	0.84[CHD][hapmap]
rs4917732	1.00[JPT][hapmap]
rs7077344	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv831950	chr10:98080972-98245434	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10882777	PLCE1	cis	cerebellum	SCAN
rs10882777	LOXL4	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98106200-98126000	Weak transcription	Aorta	Aorta
2	chr10:98115200-98119600	Active TSS	Brain Angular Gyrus	brain
3	chr10:98117000-98123800	Weak transcription	Right Atrium	heart
4	chr10:98117000-98134400	Weak transcription	Thymus	Thymus
5	chr10:98118800-98119800	Flanking Active TSS	Brain Hippocampus Middle	brain
6	chr10:98118800-98130200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:98119000-98119600	Flanking Active TSS	Brain Cingulate Gyrus	brain
8	chr10:98119200-98121200	Enhancers	Brain Anterior Caudate	brain
9	chr10:98119400-98120400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr10:98119400-98120400	Enhancers	Brain Substantia Nigra	brain

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