Variant report

Variant	rs2044545
Chromosome Location	chr11:119765318-119765319
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11217560	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217562	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12285075	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12286892	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938736	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4938737	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938738	0.96[EUR][1000 genomes]
rs517918	0.99[EUR][1000 genomes]
rs525588	0.99[EUR][1000 genomes]
rs554422	0.97[EUR][1000 genomes]
rs765814	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	nsv1051526	chr11:119750335-119775811	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1038232	chr11:119759344-119785065	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2044545	CCDC84	cis	parietal	SCAN
rs2044545	SCN2B	cis	parietal	SCAN
rs2044545	CCDC84	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119747200-119768200	Weak transcription	Fetal Intestine Small	intestine
2	chr11:119762600-119765600	Weak transcription	Esophagus	oesophagus
3	chr11:119763000-119767800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:119763000-119768400	Weak transcription	Left Ventricle	heart
5	chr11:119763000-119780800	Weak transcription	Right Atrium	heart
6	chr11:119763800-119767200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr11:119763800-119767400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:119764000-119768000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:119764200-119766000	Weak transcription	Brain Substantia Nigra	brain
10	chr11:119764200-119766200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:119764600-119768000	Weak transcription	Fetal Heart	heart

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Input of quick search could be:

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

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