Variant report

Variant	rs4291860
Chromosome Location	chr15:59784334-59784335
allele	A/C
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:5)

rs_ID	r²[population]
rs12913655	0.87[ASN][1000 genomes]
rs4238339	1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4296198	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4624109	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4774336	0.85[CHB][hapmap];0.89[JPT][hapmap]

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	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv904278	chr15:59705005-59784648	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4291860	CGNL1	cis	parietal	SCAN
rs4291860	RNF130	trans	lymphoblastoid	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59736800-59785000	Weak transcription	Fetal Brain Male	brain
2	chr15:59767600-59785000	Weak transcription	Pancreas	Pancrea
3	chr15:59771800-59784400	Weak transcription	Hela-S3	cervix
4	chr15:59775800-59785000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr15:59782000-59785000	Weak transcription	Brain Anterior Caudate	brain
6	chr15:59782400-59785600	Enhancers	Fetal Heart	heart
7	chr15:59783400-59785000	Enhancers	Brain Hippocampus Middle	brain
8	chr15:59783400-59785000	Weak transcription	Fetal Intestine Small	intestine
9	chr15:59783600-59785000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:59783600-59785000	Enhancers	Brain Cingulate Gyrus	brain
11	chr15:59783800-59784400	Weak transcription	Brain Substantia Nigra	brain
12	chr15:59783800-59785600	Enhancers	Brain Angular Gyrus	brain
13	chr15:59784000-59785200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:59784000-59788600	Weak transcription	Left Ventricle	heart
15	chr15:59784200-59785600	Enhancers	Primary B cells from cord blood	blood

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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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