Variant report

Variant	rs2516688
Chromosome Location	chr6:30364524-30364525
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1264570	0.86[EUR][1000 genomes]
rs2072111	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2516685	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2524205	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3094623	0.82[AFR][1000 genomes]
rs3129825	0.82[AFR][1000 genomes]
rs3129826	0.82[AFR][1000 genomes]
rs3129827	0.82[AFR][1000 genomes]
rs3129828	0.82[AFR][1000 genomes]
rs3132621	0.82[AFR][1000 genomes]
rs3132622	0.82[AFR][1000 genomes]
rs9261700	0.82[AFR][1000 genomes]

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	nsv1025667	chr6:30292845-30638066	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	825 gene(s)	inside rSNPs	diseases
2	nsv969293	chr6:30348821-30368580	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2516688	HCG22	cis	lymphoblastoid	seeQTL
rs2516688	HCG18	cis	multi-tissue	Pritchard
rs2516688	C6orf227	cis	cerebellum	SCAN
rs2516688	HLA-E	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30359800-30364600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:30363800-30364800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
3	chr6:30363800-30364800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:30364000-30365000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:30364000-30365200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
6	chr6:30364200-30364600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:30364400-30364600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
8	chr6:30364400-30364600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:30364400-30364800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
10	chr6:30364400-30364800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
11	chr6:30364400-30364800	Flanking Bivalent TSS/Enh	Colon Smooth Muscle	Colon
12	chr6:30364400-30364800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr6:30364400-30365000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:30364400-30365000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr6:30364400-30365000	Bivalent Enhancer	Placenta	Placenta
16	chr6:30364400-30365000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
17	chr6:30364400-30365200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr6:30364400-30365200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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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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