Variant report

Variant	rs7937779
Chromosome Location	chr11:119957107-119957108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
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]
rs3915715	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	0.86[AFR][1000 genomes];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	0.91[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]
rs7949126	1.00[ASN][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	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	nsv832285	chr11:119789595-119957724	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	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
rs7937779	FXYD2	cis	parietal	SCAN
rs7937779	POU2F3	cis	cerebellum	SCAN
rs7937779	TECTA	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119955400-119961000	Weak transcription	Esophagus	oesophagus
2	chr11:119956200-119957200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:119956400-119959200	Enhancers	Brain Angular Gyrus	brain
4	chr11:119956400-119959400	Enhancers	Brain Anterior Caudate	brain
5	chr11:119956400-119959400	Enhancers	Brain Hippocampus Middle	brain
6	chr11:119956400-119959400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr11:119956400-119959400	Enhancers	Brain Substantia Nigra	brain
8	chr11:119956400-119959800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr11:119956400-119962800	Enhancers	Brain Cingulate Gyrus	brain
10	chr11:119956600-119957600	Enhancers	Fetal Brain Male	brain
11	chr11:119956800-119957200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:119956800-119957600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:119957000-119957200	Enhancers	Fetal Muscle Leg	muscle
14	chr11:119957000-119958000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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