Variant report

Variant	rs11694407
Chromosome Location	chr2:12121262-12121263
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10460294	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10929774	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11695533	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11891008	0.82[AMR][1000 genomes]
rs12989918	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12991316	0.89[ASN][1000 genomes]
rs13003327	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13003710	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13011455	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13015144	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13019206	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13020034	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1595807	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4669792	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6712004	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs7575078	0.81[ASN][1000 genomes]
rs972873	0.91[AMR][1000 genomes];0.89[EUR][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	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv833403	chr2:11944552-12125634	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv580999	chr2:12119686-12134346	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11694407	KCNF1	cis	cerebellum	SCAN
rs11694407	IAH1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12115800-12127200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:12116400-12122600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:12120600-12122200	Enhancers	Pancreas	Pancrea
4	chr2:12120600-12122400	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr2:12120800-12121600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:12120800-12121600	Enhancers	Osteobl	bone
7	chr2:12121000-12121400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:12121000-12121600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:12121000-12121800	Enhancers	Fetal Muscle Leg	muscle

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