Variant report

Variant	rs12405609
Chromosome Location	chr1:57561775-57561776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12406184	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12407883	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12564961	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17114978	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17115023	1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17115030	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17419873	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17420013	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17420181	1.00[CHB][hapmap]
rs17420216	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17453874	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs35522019	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55706301	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61765294	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61765295	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61765319	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61765320	0.81[ASN][1000 genomes]
rs6697173	1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728719	1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.93[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	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
rs12405609	TRAP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57548800-57566600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:57549600-57566600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
4	chr1:57556800-57568800	Weak transcription	Right Atrium	heart
5	chr1:57558000-57564800	Weak transcription	Fetal Intestine Large	intestine
6	chr1:57559000-57568600	Weak transcription	Left Ventricle	heart
7	chr1:57560000-57562600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:57561000-57562800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:57561200-57562200	Enhancers	Fetal Heart	heart
10	chr1:57561600-57562400	Enhancers	Fetal Brain Female	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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