Variant report

Variant	rs9257940
Chromosome Location	chr6:29642509-29642510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2071652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071653	0.83[ASN][1000 genomes]
rs3095291	0.84[ASN][1000 genomes]
rs3117290	0.84[ASN][1000 genomes]
rs3131854	0.83[ASN][1000 genomes]
rs6905408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257927	0.91[AMR][1000 genomes]
rs9257932	0.80[EUR][1000 genomes]
rs9257953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9257986	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258004	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9258130	0.83[ASN][1000 genomes]
rs9258132	0.83[ASN][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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9257940	HLA-F	cis	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29630800-29643200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:29636400-29643800	Weak transcription	Fetal Heart	heart
4	chr6:29636600-29644800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:29637000-29644400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:29638800-29644400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:29639600-29647400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:29639800-29643400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:29640600-29643800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr6:29640800-29643000	Weak transcription	NHEK	skin
11	chr6:29641600-29643000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:29642000-29642600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr6:29642400-29643400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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