Variant report

Variant	rs9473583
Chromosome Location	chr6:49491305-49491306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12190495	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3957334	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3997172	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60944851	0.82[AMR][1000 genomes];0.84[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	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv885881	chr6:49439805-49575141	Weak transcription Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9473583	CENPQ	Cis_1M	lymphoblastoid	RTeQTL
rs9473583	MUT	Cis_1M	lymphoblastoid	RTeQTL
rs9473583	MUT	cis	lymphoblastoid	seeQTL
rs9473583	CENPQ	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49484200-49496000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:49489400-49496400	Enhancers	Liver	Liver
3	chr6:49490200-49491600	Enhancers	A549	lung
4	chr6:49490400-49491800	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr6:49490800-49491400	Enhancers	Pancreas	Pancrea
6	chr6:49491000-49491400	Enhancers	Gastric	stomach
7	chr6:49491000-49491400	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr6:49491000-49491400	Flanking Active TSS	HepG2	liver
9	chr6:49491000-49491600	Enhancers	Fetal Intestine Large	intestine
10	chr6:49491000-49492200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr6:49491000-49492400	Enhancers	Stomach Mucosa	stomach
12	chr6:49491000-49492600	Enhancers	Fetal Intestine Small	intestine

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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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