Variant report

Variant	rs58409825
Chromosome Location	chr19:19376724-19376725
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NCAN-1	chr19:19376595-19377728	ENSG00000250450

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10402729	1.00[AMR][1000 genomes]
rs10410340	0.87[AMR][1000 genomes]
rs10413995	1.00[AMR][1000 genomes]
rs10414307	0.85[AMR][1000 genomes]
rs10414990	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416520	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10417330	1.00[AMR][1000 genomes]
rs10422620	0.87[AMR][1000 genomes]
rs10423659	0.87[AMR][1000 genomes]
rs10425084	1.00[AMR][1000 genomes]
rs12327663	0.87[AMR][1000 genomes]
rs13344498	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16996031	0.87[AMR][1000 genomes]
rs28437425	0.87[AMR][1000 genomes]
rs28857503	0.87[AMR][1000 genomes]
rs4563151	0.87[AMR][1000 genomes]
rs55877107	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs55937418	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs57002012	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59049499	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]

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	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS 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	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv911306	chr19:19366643-19391838	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19373000-19384000	Weak transcription	Pancreas	Pancrea
2	chr19:19374000-19383400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr19:19374000-19383400	Weak transcription	Right Atrium	heart
4	chr19:19374200-19383600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:19374400-19381400	Strong transcription	Duodenum Mucosa	Duodenum
6	chr19:19374400-19383200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr19:19374800-19381800	Strong transcription	Fetal Intestine Small	intestine
8	chr19:19374800-19383200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:19375000-19378800	Strong transcription	Liver	Liver
10	chr19:19375400-19377800	Strong transcription	Fetal Intestine Large	intestine
11	chr19:19375800-19377200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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