Variant report

Variant	rs11716961
Chromosome Location	chr3:49908338-49908339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11711814	1.00[EUR][1000 genomes]
rs11717829	0.87[EUR][1000 genomes]
rs4688759	0.85[EUR][1000 genomes]
rs73079018	0.86[AMR][1000 genomes]
rs73079033	0.85[AMR][1000 genomes];1.00[EUR][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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11716961	WDR6	cis	Adipose Subcutaneous	GTEx
rs11716961	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs11716961	WDR6	cis	Whole Blood	GTEx
rs11716961	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs11716961	WDR6	cis	Esophagus Mucosa	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49906600-49910800	Enhancers	Fetal Brain Male	brain
2	chr3:49907600-49908600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:49907600-49909000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49907600-49909400	Enhancers	Brain Angular Gyrus	brain
5	chr3:49907600-49909400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:49907600-49910800	Weak transcription	Gastric	stomach
7	chr3:49907800-49908400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:49907800-49908600	Bivalent Enhancer	Fetal Intestine Small	intestine
9	chr3:49907800-49908800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:49907800-49909600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:49907800-49911000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:49907800-49911200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:49908000-49909400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:49908000-49910000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:49908000-49911200	Enhancers	Fetal Brain Female	brain
16	chr3:49908000-49913600	Enhancers	Fetal Intestine Large	intestine
17	chr3:49908200-49908400	Bivalent/Poised TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:49908200-49909600	Enhancers	Brain Hippocampus Middle	brain
19	chr3:49908200-49911600	Enhancers	Brain Anterior Caudate	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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