Variant report

Variant	rs17865676
Chromosome Location	chr2:234912293-234912294
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11562942	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17866591	0.88[CEU][hapmap]
rs17874956	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28605673	1.00[AFR][1000 genomes]
rs28902238	0.88[CEU][hapmap]
rs763379	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs763380	0.88[CEU][hapmap]

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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17865676	HPVC1	trans	lymphoblastoid	seeQTL
rs17865676	FAM75C1	trans	lymphoblastoid	seeQTL
rs17865676	GOLGA6L6	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234898600-234912400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:234903000-234912400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:234908400-234912600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:234909600-234912600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:234909600-234919000	Strong transcription	Liver	Liver
6	chr2:234911200-234912400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:234912000-234912600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:234912000-234912600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:234912000-234912600	Enhancers	A549	lung
10	chr2:234912000-234914000	Enhancers	NHDF-Ad	bronchial
11	chr2:234912200-234912400	Flanking Active TSS	Osteobl	bone
12	chr2:234912200-234912800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:234912200-234913600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:234912200-234913600	Enhancers	NH-A	brain

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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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