Variant report

Variant	rs59436654
Chromosome Location	chr1:174746513-174746514
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174745184..174748890-chr1:174754074..174756600,3	MCF-7	breast:
2	chr1:174740970..174743035-chr1:174745224..174747898,3	K562	blood:
3	chr1:174746135..174748853-chr1:174967335..174969373,2	MCF-7	breast:
4	chr1:174741517..174743035-chr1:174745224..174747898,2	K562	blood:

Variant related genes	Relation type
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10489332	0.83[AFR][1000 genomes]
rs16847206	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2179108	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2179109	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3753562	0.87[AFR][1000 genomes]
rs41266052	0.83[EUR][1000 genomes]
rs41498747	0.87[AFR][1000 genomes]
rs4565668	0.81[AFR][1000 genomes]
rs56864802	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57053120	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57243929	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57648142	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57898822	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58762254	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59190079	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59354288	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60240702	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60665754	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60723087	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60865584	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60885521	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61028529	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61329817	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6673649	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6692753	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6695956	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6700434	0.95[AFR][1000 genomes]
rs6703536	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7543502	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv548198	chr1:174731596-174800872	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59436654	RABGAP1L	Cis_1M	lymphoblastoid	RTeQTL
rs59436654	CRYM	trans	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174742400-174752200	Weak transcription	Fetal Intestine Small	intestine
2	chr1:174742600-174746800	Weak transcription	Fetal Intestine Large	intestine
3	chr1:174745000-174756800	Weak transcription	HSMMtube	muscle
4	chr1:174745600-174747000	Enhancers	Primary B cells from cord blood	blood
5	chr1:174745800-174747200	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links