Variant report

Variant	rs12289146
Chromosome Location	chr11:93575238-93575239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11020531	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12290442	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12290507	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs671490	0.93[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.95[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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12289146	C11orf54	cis	lymphoblastoid	seeQTL
rs12289146	SCARNA9	cis	parietal	SCAN
rs12289146	C11orf54	cis	cerebellum	SCAN
rs12289146	MED17	cis	parietal	SCAN
rs12289146	C11orf54	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93565400-93575400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr11:93566200-93577000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:93567800-93575600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:93570400-93579200	Enhancers	Stomach Mucosa	stomach
5	chr11:93572600-93582800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:93573200-93577000	Weak transcription	Placenta	Placenta
7	chr11:93573600-93575400	Weak transcription	HSMMtube	muscle
8	chr11:93574200-93577400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:93574400-93576000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:93574400-93582800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:93574600-93575600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:93574800-93579800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:93575000-93575600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:93575000-93575800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr11:93575200-93576600	Enhancers	Rectal Mucosa Donor 31	rectum

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

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