Variant report

Variant	rs3915715
Chromosome Location	chr11:119960260-119960261
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12273529	1.00[ASN][1000 genomes]
rs12285338	1.00[ASN][1000 genomes]
rs12418021	1.00[CHB][hapmap]
rs1349688	1.00[CHB][hapmap]
rs3895896	0.98[EUR][1000 genomes]
rs4938776	0.97[EUR][1000 genomes]
rs4938779	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60480291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897956	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897958	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897959	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61900463	1.00[ASN][1000 genomes]
rs7111010	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7929336	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7937779	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949126	1.00[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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv508657	chr11:119891578-119971212	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3915715	FXYD2	cis	parietal	SCAN
rs3915715	TECTA	cis	cerebellum	SCAN
rs3915715	POU2F3	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119955400-119961000	Weak transcription	Esophagus	oesophagus
2	chr11:119956400-119962800	Enhancers	Brain Cingulate Gyrus	brain
3	chr11:119958600-119961800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:119959200-119960600	Weak transcription	Brain Angular Gyrus	brain
5	chr11:119959600-119960600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:119959800-119961400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:119960000-119960400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:119960000-119960400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr11:119960000-119961000	Weak transcription	Pancreas	Pancrea
10	chr11:119960000-119961200	Weak transcription	Aorta	Aorta
11	chr11:119960000-119961200	Weak transcription	Left Ventricle	heart
12	chr11:119960000-119961200	Weak transcription	Right Ventricle	heart
13	chr11:119960000-119963400	Enhancers	Brain Anterior Caudate	brain
14	chr11:119960000-119963600	Enhancers	Brain Substantia Nigra	brain
15	chr11:119960200-119960800	Enhancers	Brain Hippocampus Middle	brain
16	chr11:119960200-119964400	Enhancers	Breast Myoepithelial Primary Cells	Breast

Quick Search:

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

what's new

Quick links