Variant report

Variant	rs12637828
Chromosome Location	chr3:54231618-54231619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11929236	0.83[EUR][1000 genomes]
rs12495373	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28458274	0.83[ASN][1000 genomes]
rs4485754	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55886209	0.82[EUR][1000 genomes]
rs56343815	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6807607	0.88[CEU][hapmap];0.85[GIH][hapmap];0.83[EUR][1000 genomes]
rs73085965	0.85[ASN][1000 genomes]
rs7617542	0.83[EUR][1000 genomes]
rs7640196	0.81[CEU][hapmap];0.85[GIH][hapmap];0.83[EUR][1000 genomes]
rs9825455	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs9846549	0.81[CEU][hapmap]
rs9851662	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9879718	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers 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	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1014157	chr3:54168755-54332321	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv518483	chr3:54212182-54259801	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12637828	POC1A	cis	parietal	SCAN
rs12637828	RPL29	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54227200-54232200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:54227600-54232600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:54227800-54232600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:54228000-54232200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:54229400-54233000	Enhancers	Brain Germinal Matrix	brain
6	chr3:54231000-54232800	Weak transcription	Fetal Brain Male	brain

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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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