Variant report

Variant	rs12997170
Chromosome Location	chr2:12227218-12227219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10183374	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10190465	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10495590	0.83[ASN][1000 genomes]
rs12474091	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3845756	0.84[ASN][1000 genomes]
rs62113831	0.82[ASN][1000 genomes]
rs7419959	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv999704	chr2:12153766-12243960	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1005069	chr2:12161023-12242734	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1000696	chr2:12162843-12241022	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv997538	chr2:12216408-12242734	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12997170	AC012456.4	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:12217400-12249800	Weak transcription	GM12878-XiMat	blood
2	chr2:12221000-12234200	Weak transcription	Spleen	Spleen
3	chr2:12223800-12227400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:12224000-12227400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:12224400-12230800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:12224600-12236400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:12224800-12229600	Weak transcription	Brain Germinal Matrix	brain
8	chr2:12224800-12238000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:12226800-12228400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:12227000-12228200	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:12227000-12228200	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr2:12227000-12228200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:12227200-12229200	Enhancers	NHEK	skin
14	chr2:12227200-12229400	Enhancers	HMEC	breast

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

what's new

Quick links