Variant report

Variant	rs561124
Chromosome Location	chr22:27668633-27668634
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16983778	1.00[MEX][hapmap]
rs483136	1.00[AMR][1000 genomes]
rs526404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs527223	1.00[AMR][1000 genomes]
rs530083	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs541153	1.00[AMR][1000 genomes]
rs545268	1.00[AMR][1000 genomes]
rs553032	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs562230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs562896	1.00[AMR][1000 genomes]
rs57875447	1.00[AMR][1000 genomes]
rs73428210	1.00[AMR][1000 genomes]
rs73428213	1.00[AMR][1000 genomes]
rs849355	1.00[AMR][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	nsv917333	chr22:26931825-27692024	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	142 gene(s)	inside rSNPs	diseases
2	esv34168	chr22:27289097-27678031	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3413125	chr22:27404463-28121577	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv459860	chr22:27527005-28181436	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv588872	chr22:27527005-28181436	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv834166	chr22:27628570-27814359	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs561124	ICOS	trans	lymphoblastoid	seeQTL
rs561124	FAM153C	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:27665200-27670000	Weak transcription	Spleen	Spleen
2	chr22:27666000-27669400	Enhancers	Brain Germinal Matrix	brain
3	chr22:27666400-27671800	Enhancers	Fetal Brain Male	brain
4	chr22:27666800-27669000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr22:27667000-27668800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr22:27667200-27668800	Weak transcription	Pancreas	Pancrea
7	chr22:27667200-27669200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr22:27667200-27669400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:27667400-27669000	Weak transcription	Ovary	ovary
10	chr22:27667400-27669400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:27668200-27670000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:27668400-27669200	Enhancers	Fetal Brain Female	brain
13	chr22:27668600-27669000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr22:27668600-27671800	Enhancers	Cortex derived primary cultured neurospheres	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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