Variant report

Variant	rs878904
Chromosome Location	chr11:76026586-76026587
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10899206	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11236699	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1893916	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2004607	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2156715	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2213019	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2618087	0.84[EUR][1000 genomes]
rs2618088	0.85[EUR][1000 genomes]
rs4564359	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736981	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736982	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750802	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897930	chr11:75960472-76027936	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs878904	INTS4	cis	cerebellum	SCAN
rs878904	KCTD21	cis	parietal	SCAN
rs878904	FOLR3	cis	parietal	SCAN
rs878904	PGM2L1	cis	parietal	SCAN
rs878904	FABP7	trans	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76024400-76027000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr11:76024800-76026800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:76025000-76026600	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr11:76025000-76026800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:76025000-76027000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:76025000-76027000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:76025200-76026800	Enhancers	HMEC	breast
8	chr11:76025200-76026800	Enhancers	NHEK	skin
9	chr11:76025400-76026600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:76025400-76027000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:76025400-76029800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:76025800-76028400	Weak transcription	Hela-S3	cervix
13	chr11:76025800-76029200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:76025800-76031200	Weak transcription	Placenta	Placenta
15	chr11:76026000-76028400	Weak transcription	Adipose Nuclei	Adipose
16	chr11:76026200-76026800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr11:76026200-76029400	Weak transcription	Fetal Lung	lung

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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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