Variant report

Variant	rs12099462
Chromosome Location	chr12:48503104-48503105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10875743	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875749	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168408	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168428	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12228750	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12368659	0.81[EUR][1000 genomes]
rs1476607	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2051851	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3997	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4760679	0.82[EUR][1000 genomes]
rs7139330	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7301003	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8716	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs973398	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9971924	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12099462	H1FNT	cis	Muscle Skeletal	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48501000-48503600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:48501000-48504000	Weak transcription	Psoas Muscle	Psoas
3	chr12:48501000-48504200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:48501000-48504800	Weak transcription	Lung	lung
5	chr12:48501000-48508800	Weak transcription	K562	blood
6	chr12:48501200-48503200	Weak transcription	Hela-S3	cervix
7	chr12:48501200-48503400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:48501200-48503400	Weak transcription	Spleen	Spleen
9	chr12:48501200-48504600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:48501200-48512200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:48501400-48503800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:48501600-48506600	Weak transcription	Fetal Intestine Small	intestine
13	chr12:48501800-48503200	Weak transcription	HepG2	liver
14	chr12:48502000-48503400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:48502000-48503800	Enhancers	GM12878-XiMat	blood
16	chr12:48503000-48504400	Enhancers	HMEC	breast

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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