Variant report

Variant	rs2840586
Chromosome Location	chr1:159927408-159927409
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
SLAMF9	TF binding region
LINC01133	TF binding region
ENSG00000085552	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000162723	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2789415	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2789416	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2789417	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2789418	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2789420	0.89[EUR][1000 genomes]
rs2820579	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2820584	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2840581	0.86[AMR][1000 genomes]
rs2840583	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3001288	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4402127	0.86[AMR][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	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv548055	chr1:159918418-159940000	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv520773	chr1:159922959-159935569	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159916200-159930600	Weak transcription	Right Atrium	heart
2	chr1:159919800-159930400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:159924000-159927800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:159924000-159928800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:159924000-159928800	Weak transcription	Esophagus	oesophagus
6	chr1:159924200-159928400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:159924400-159929200	Weak transcription	Osteobl	bone
8	chr1:159925200-159929600	Weak transcription	NHDF-Ad	bronchial
9	chr1:159925400-159929000	Weak transcription	HMEC	breast
10	chr1:159925600-159927800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:159926200-159927600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:159926400-159927800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:159926400-159928800	Weak transcription	NHEK	skin
14	chr1:159927000-159927800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:159927200-159927800	Enhancers	K562	blood
16	chr1:159927200-159929600	Enhancers	Fetal Intestine Small	intestine

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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

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