Variant report

Variant	rs2654194
Chromosome Location	chr15:82364871-82364872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2654191	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2654192	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2654193	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2654195	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2654197	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2654226	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2665088	0.87[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2665091	0.81[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2665098	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2665101	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2665102	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833067	chr15:82234980-82450485	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv2422504	chr15:82293064-82426400	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv457211	chr15:82362125-82396347	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv570241	chr15:82362125-82396347	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2654194	BTBD1	cis	parietal	SCAN
rs2654194	ACSBG1	cis	cerebellum	SCAN
rs2654194	ZFAND6	cis	parietal	SCAN
rs2654194	HMG20A	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:82364200-82366000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:82364400-82366200	Enhancers	K562	blood

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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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