Variant report

Variant	rs11125094
Chromosome Location	chr2:47060312-47060313
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10173681	1.00[CEU][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs10177650	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12469521	0.83[JPT][hapmap]
rs35828414	0.80[ASN][1000 genomes]
rs72884735	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv817840	chr2:47044218-47070827	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11125094	MCFD2	cis	parietal	SCAN
rs11125094	MCFD2	cis	cerebellum	SCAN
rs11125094	SLC3A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47055000-47063200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:47055400-47062800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:47055400-47063000	Weak transcription	Right Ventricle	heart
4	chr2:47056600-47062800	Weak transcription	Right Atrium	heart
5	chr2:47057200-47062400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:47058800-47063000	Weak transcription	NH-A	brain
7	chr2:47059400-47062600	Weak transcription	Placenta	Placenta
8	chr2:47059400-47063000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:47059400-47063000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:47059600-47060400	Genic enhancers	Osteobl	bone
11	chr2:47059800-47062600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:47059800-47063000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:47060000-47061000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:47060000-47063000	Weak transcription	NHLF	lung
15	chr2:47060000-47063400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr2:47060200-47063200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:47060200-47070400	Weak transcription	NHDF-Ad	bronchial

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