Variant report

Variant	rs17115023
Chromosome Location	chr1:57566233-57566234
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:57561067..57563455-chr1:57563927..57566507,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11206975	1.00[CEU][hapmap]
rs11206981	1.00[CEU][hapmap]
rs12405609	1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12406184	0.80[ASN][1000 genomes]
rs12407883	0.80[ASN][1000 genomes]
rs12408256	1.00[CEU][hapmap]
rs12562392	1.00[CEU][hapmap]
rs12562394	1.00[CEU][hapmap]
rs12562609	1.00[CEU][hapmap]
rs12562930	1.00[CEU][hapmap]
rs12563280	1.00[CEU][hapmap]
rs12564278	1.00[CEU][hapmap]
rs12564961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12566131	1.00[CEU][hapmap]
rs12566320	1.00[CEU][hapmap]
rs12567335	1.00[CEU][hapmap]
rs12567531	1.00[CEU][hapmap]
rs12567904	1.00[CEU][hapmap]
rs12568148	1.00[CEU][hapmap]
rs12568862	1.00[CEU][hapmap]
rs17114840	1.00[JPT][hapmap]
rs17114978	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115000	0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs17115030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17115105	1.00[CEU][hapmap]
rs17115108	1.00[CEU][hapmap]
rs17115146	1.00[CEU][hapmap]
rs17115155	1.00[CEU][hapmap]
rs17115222	1.00[CEU][hapmap]
rs17115397	1.00[CEU][hapmap]
rs17419873	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17420013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17420181	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17420216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17421219	1.00[CEU][hapmap]
rs17421839	1.00[CEU][hapmap]
rs17422039	1.00[CEU][hapmap]
rs17453874	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17455073	1.00[CEU][hapmap]
rs17455469	1.00[CEU][hapmap]
rs17455616	1.00[CEU][hapmap]
rs17455728	1.00[CEU][hapmap]
rs17455840	1.00[CEU][hapmap]
rs35522019	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55706301	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61765294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61765295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61765319	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61765320	0.87[ASN][1000 genomes]
rs6697173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs728719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.97[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	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
rs17115023	TRAP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 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	chr1:57559000-57568600	Weak transcription	Left Ventricle	heart
6	chr1:57562200-57567000	Weak transcription	Fetal Heart	heart
7	chr1:57562400-57567000	Weak transcription	Fetal Brain Female	brain
8	chr1:57563200-57566600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:57565600-57569000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links