Variant report

Variant	rs9448820
Chromosome Location	chr6:80488590-80488591
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:80488032..80490000-chr6:80496422..80499072,2	K562	blood:
2	chr6:80487847..80488706-chr6:80578916..80579523,2	MCF-7	breast:
3	chr6:80487310..80489251-chr6:80525318..80527015,2	MCF-7	breast:
4	chr6:80487168..80488775-chr6:80523270..80524422,9	MCF-7	breast:
5	chr6:80481025..80482615-chr6:80488324..80491118,2	MCF-7	breast:
6	chr6:80487640..80488609-chr6:80577520..80578268,3	MCF-7	breast:
7	chr6:80488349..80490250-chr6:80492634..80494857,2	MCF-7	breast:
8	chr6:80487463..80488809-chr6:80523025..80524264,5	K562	blood:
9	chr6:80488189..80489092-chr6:80579221..80580068,2	K562	blood:

No data

No data

No data

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12660740	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4467741	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59337495	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6921089	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6925255	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6941826	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs714701	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs714702	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714703	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714704	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs720808	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7768071	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs926839	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9350827	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9352765	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9361558	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9443716	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1021143	chr6:80400195-80598163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv886305	chr6:80433732-80495689	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9448820	HMGN3	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80487400-80488600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:80487400-80488600	Enhancers	Fetal Heart	heart
3	chr6:80488200-80488600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:80488200-80488600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:80488200-80488600	Enhancers	Liver	Liver
6	chr6:80488200-80488600	Enhancers	Fetal Intestine Large	intestine
7	chr6:80488200-80495200	Weak transcription	Right Atrium	heart
8	chr6:80488400-80489000	Bivalent Enhancer	HepG2	liver
9	chr6:80488400-80502200	Weak transcription	Fetal Brain Male	brain

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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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