Variant report

Variant	rs12685019
Chromosome Location	chr9:92748385-92748386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12685781	0.93[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34954114	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4744002	0.85[ASN][1000 genomes]
rs4744499	0.85[ASN][1000 genomes]
rs662867	0.88[ASN][1000 genomes]
rs7027794	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9650758	0.85[ASN][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	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12685019	HCK	trans	lymphoblastoid	seeQTL
rs12685019	C9orf153	cis	cerebellum	SCAN
rs12685019	ZNF484	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92745000-92752800	Weak transcription	Liver	Liver
2	chr9:92745000-92755400	Weak transcription	Psoas Muscle	Psoas
3	chr9:92745400-92748600	Enhancers	HMEC	breast
4	chr9:92747600-92750200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr9:92747600-92750400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr9:92747600-92750800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:92747600-92751400	Weak transcription	Right Atrium	heart
8	chr9:92747600-92753200	Weak transcription	NHEK	skin
9	chr9:92747800-92748400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:92747800-92750000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr9:92747800-92750000	Weak transcription	HSMM	muscle
12	chr9:92747800-92750000	Weak transcription	HSMMtube	muscle
13	chr9:92748000-92748800	Enhancers	Esophagus	oesophagus
14	chr9:92748200-92749000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

Quick Search:

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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