Variant report

Variant	rs9378220
Chromosome Location	chr6:30077135-30077136
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 6 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3734837	0.83[EUR][1000 genomes]
rs62390186	0.84[EUR][1000 genomes]
rs62390201	0.83[EUR][1000 genomes]
rs62390202	0.83[EUR][1000 genomes]
rs9366753	0.81[EUR][1000 genomes]

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	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9378220	HLA-H	cis	lymphoblastoid	seeQTL
rs9378220	HLA-A	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30071600-30079200	Weak transcription	Gastric	stomach
2	chr6:30072200-30078000	Weak transcription	Colonic Mucosa	Colon
3	chr6:30075800-30078000	Weak transcription	Fetal Intestine Small	intestine
4	chr6:30076000-30079400	Weak transcription	Hela-S3	cervix
5	chr6:30076600-30077200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
6	chr6:30077000-30077200	Active TSS	Sigmoid Colon	Sigmoid Colon
7	chr6:30077000-30077200	Active TSS	Stomach Mucosa	stomach

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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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