Variant report

Variant	rs11788050
Chromosome Location	chr9:98799475-98799476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12684445	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743472	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4743479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72743922	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
2	nsv524266	chr9:98780606-98804274	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3382610	chr9:98798281-98800379	ZNF genes & repeats Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv1809137	chr9:98798752-98823646	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11788050	LINC00476	cis	Whole Blood	GTEx
rs11788050	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98790800-98810800	Weak transcription	Brain Angular Gyrus	brain
2	chr9:98793600-98800800	Weak transcription	Brain Substantia Nigra	brain
3	chr9:98793600-98804600	Weak transcription	Fetal Heart	heart
4	chr9:98794400-98801000	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:98796800-98802000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr9:98798000-98800600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:98798200-98801000	Weak transcription	Fetal Lung	lung
8	chr9:98798800-98802400	Weak transcription	Fetal Brain Male	brain
9	chr9:98799200-98804600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:98799400-98800000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:98799400-98800000	Enhancers	Pancreas	Pancrea

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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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