Variant report

Variant	rs12819124
Chromosome Location	chr12:48409054-48409055
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11168351	0.89[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12579815	1.00[JPT][hapmap]
rs12580309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12581263	0.91[ASN][1000 genomes]
rs17122615	1.00[JPT][hapmap]
rs17122617	1.00[JPT][hapmap]
rs2408955	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs41272785	0.83[ASN][1000 genomes]
rs41369448	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs60275794	0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12819124	PRPF40B	cis	parietal	SCAN
rs12819124	PFKM	cis	parietal	SCAN
rs12819124	H1FNT	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48399400-48415000	Weak transcription	Right Atrium	heart
2	chr12:48403000-48410200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48407600-48411400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:48407800-48410800	Weak transcription	Fetal Intestine Small	intestine
5	chr12:48408400-48409400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr12:48408800-48410600	Weak transcription	Fetal Intestine Large	intestine

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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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