Variant report

Variant	rs12913391
Chromosome Location	chr15:56342436-56342437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs33999564	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34346596	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35614491	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35651536	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35757723	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67156824	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][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	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12913391	IRGC	trans	parietal	SCAN
rs12913391	USP50	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56337400-56344600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:56337800-56342800	Weak transcription	Hela-S3	cervix
3	chr15:56339800-56342800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:56340000-56343800	Weak transcription	NHEK	skin
5	chr15:56340000-56344400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:56340200-56344600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:56340200-56344600	Weak transcription	HMEC	breast
8	chr15:56340800-56344800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:56341400-56342800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:56341600-56342600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:56341800-56342800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:56341800-56343000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:56341800-56344600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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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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