Variant report

Variant	rs16841682
Chromosome Location	chr1:159064818-159064819
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12098223	0.82[GIH][hapmap]
rs12124059	0.83[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs12239437	1.00[TSI][hapmap]
rs16841642	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1935067	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298803	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2518562	0.89[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2793845	0.81[ASN][1000 genomes]
rs3737522	0.82[GIH][hapmap]
rs3754460	0.82[GIH][hapmap]
rs3768513	0.81[GIH][hapmap]
rs41264457	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55719948	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55791394	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs855865	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs855871	0.83[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16841682	AIM2	cis	multi-tissue	Pritchard
rs16841682	AIM2	Cis_1M	lymphoblastoid	RTeQTL
rs16841682	AIM2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159062600-159065000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:159062800-159065800	Weak transcription	HUVEC	blood vessel
3	chr1:159063200-159065200	Weak transcription	NHEK	skin
4	chr1:159063400-159065000	Weak transcription	HMEC	breast
5	chr1:159063400-159065200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:159063400-159067000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr1:159063400-159067000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:159064400-159066800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:159064600-159065400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:159064800-159065400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:159064800-159065400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:159064800-159065400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:159064800-159065400	Enhancers	NHDF-Ad	bronchial
14	chr1:159064800-159066000	Enhancers	Osteobl	bone
15	chr1:159064800-159066800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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