Variant report

Variant	rs2278717
Chromosome Location	chr2:113816942-113816943
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10165821	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11687093	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11687630	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11687786	0.92[ASN][1000 genomes]
rs12618939	0.92[ASN][1000 genomes]
rs12995447	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13019891	0.84[CHB][hapmap];0.81[AMR][1000 genomes]
rs1374280	0.88[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs1867834	0.84[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS 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	12 gene(s)	inside rSNPs	diseases
5	nsv2881	chr2:113800805-113846597	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2278717	LOC654433	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113814600-113818400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:113815800-113817400	Enhancers	NHEK	skin
3	chr2:113816000-113817000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:113816000-113817000	Enhancers	HMEC	breast
5	chr2:113816000-113818400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:113816200-113817000	Enhancers	Placenta	Placenta
7	chr2:113816200-113817600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:113816400-113817200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:113816400-113817400	Enhancers	Fetal Lung	lung
10	chr2:113816400-113817800	Enhancers	Placenta Amnion	Placenta Amnion
11	chr2:113816800-113817400	Flanking Active TSS	Esophagus	oesophagus

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