Variant report

Variant	rs4513910
Chromosome Location	chr7:78081432-78081433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10485888	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[ASN][1000 genomes]
rs10953565	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs17150823	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs17431054	0.96[ASN][1000 genomes]
rs2110869	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2110870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2160319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2885553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4319010	0.93[CEU][hapmap];0.98[EUR][1000 genomes]
rs73148374	0.98[EUR][1000 genomes]
rs7794878	0.99[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	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4513910	CACNA2D1	cis	parietal	SCAN
rs4513910	PHTF2	cis	cerebellum	SCAN
rs4513910	PHTF2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78078600-78082400	Weak transcription	Brain Hippocampus Middle	brain
2	chr7:78078800-78082400	Weak transcription	Brain Substantia Nigra	brain
3	chr7:78079000-78082400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:78080200-78082400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:78080200-78082400	Weak transcription	Brain Anterior Caudate	brain
6	chr7:78080400-78082400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr7:78080600-78082000	Weak transcription	Brain Angular Gyrus	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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