Variant report

Variant	rs1552511
Chromosome Location	chr11:92605986-92605987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10830951	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12277422	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12294687	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3912662	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043861	chr11:92357570-92689868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1044571	chr11:92495213-92742314	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1552511	SNORD5	cis	parietal	SCAN
rs1552511	SNORA40	cis	parietal	SCAN
rs1552511	SRSF8	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:92586800-92615800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:92587400-92615800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:92590400-92615800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:92593800-92615400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:92597400-92606000	Strong transcription	Fetal Lung	lung
6	chr11:92598800-92607400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:92599000-92607000	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:92599000-92615800	Weak transcription	Fetal Stomach	stomach
9	chr11:92599200-92611000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:92599200-92616200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:92600600-92615800	Weak transcription	Fetal Brain Female	brain
12	chr11:92600800-92615800	Weak transcription	Aorta	Aorta
13	chr11:92601400-92606200	Weak transcription	Fetal Brain Male	brain
14	chr11:92601800-92623800	Weak transcription	Brain Anterior Caudate	brain
15	chr11:92602000-92612400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:92604000-92611200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:92605600-92608400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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