Variant report

Variant	rs4938780
Chromosome Location	chr11:119976805-119976806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1073634	0.83[AFR][1000 genomes]
rs1073636	0.83[AFR][1000 genomes]
rs10892538	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1107149	0.83[AFR][1000 genomes]
rs1110703	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1110704	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1110705	0.84[AFR][1000 genomes]
rs12418021	1.00[CHB][hapmap]
rs1349688	1.00[CHB][hapmap]
rs2368961	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6589798	0.82[AFR][1000 genomes]
rs6589799	0.82[AFR][1000 genomes]
rs6589800	0.82[AFR][1000 genomes]
rs6589801	0.83[AFR][1000 genomes]
rs6589802	0.83[AFR][1000 genomes]
rs7131339	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7131629	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7938843	0.96[EUR][1000 genomes]
rs7946597	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];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	nsv1050132	chr11:119976310-120010437	Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4938780	TREH	cis	cerebellum	SCAN
rs4938780	SC5DL	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119966800-119978200	Weak transcription	Brain Substantia Nigra	brain
2	chr11:119973800-119978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:119975200-119977000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:119975200-119980400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr11:119975400-119977000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:119976400-119977000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:119976400-119978400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:119976400-119979400	Enhancers	Brain Cingulate Gyrus	brain
9	chr11:119976400-119979400	Enhancers	Brain Hippocampus Middle	brain
10	chr11:119976400-119979600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr11:119976600-119979600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:119976800-119977800	Weak transcription	Brain Angular Gyrus	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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