Variant report

Variant	rs9535058
Chromosome Location	chr13:49194583-49194584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1009719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050047	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12583212	0.94[ASN][1000 genomes]
rs12583622	0.94[ASN][1000 genomes]
rs12585234	0.94[ASN][1000 genomes]
rs12855185	0.84[EUR][1000 genomes]
rs12859099	0.85[EUR][1000 genomes]
rs12864882	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12867110	0.94[ASN][1000 genomes]
rs12867640	0.94[ASN][1000 genomes]
rs12870838	0.91[ASN][1000 genomes]
rs12870872	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12871411	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12871822	0.92[ASN][1000 genomes]
rs12876715	0.92[ASN][1000 genomes]
rs12876717	0.82[EUR][1000 genomes]
rs12877288	0.83[EUR][1000 genomes]
rs1326697	0.98[ASN][1000 genomes]
rs1359107	0.84[ASN][1000 genomes]
rs1476406	0.92[ASN][1000 genomes]
rs1808060	0.82[EUR][1000 genomes]
rs1980838	0.90[ASN][1000 genomes]
rs1980839	0.90[ASN][1000 genomes]
rs198563	0.80[CEU][hapmap]
rs198584	0.80[CEU][hapmap]
rs198590	0.80[CEU][hapmap]
rs2146861	0.90[ASN][1000 genomes]
rs2148516	0.98[ASN][1000 genomes]
rs34119347	0.94[ASN][1000 genomes]
rs36088391	0.94[ASN][1000 genomes]
rs59136233	0.98[ASN][1000 genomes]
rs59927903	0.92[ASN][1000 genomes]
rs7331325	0.94[ASN][1000 genomes]
rs7987608	0.87[ASN][1000 genomes]
rs7988330	0.94[ASN][1000 genomes]
rs7989251	0.87[ASN][1000 genomes]
rs9316381	0.80[CEU][hapmap]
rs9316388	0.80[CEU][hapmap]
rs9316407	0.84[EUR][1000 genomes]
rs9535049	0.83[EUR][1000 genomes]
rs9535055	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535056	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535061	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9562835	0.82[ASN][1000 genomes]
rs9562836	0.82[ASN][1000 genomes]
rs9568057	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568060	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568063	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568066	0.92[ASN][1000 genomes]
rs9568067	0.98[ASN][1000 genomes]
rs9568068	0.98[ASN][1000 genomes]
rs9568070	0.92[ASN][1000 genomes]
rs9568071	0.98[ASN][1000 genomes]
rs9568072	0.92[ASN][1000 genomes]
rs9568075	0.94[ASN][1000 genomes]
rs9568077	0.82[ASN][1000 genomes]
rs9634815	0.94[ASN][1000 genomes]
rs9634816	0.94[ASN][1000 genomes]
rs9634817	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3495983	chr13:49181790-49222165	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3495984	chr13:49181790-49222165	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9535058	ITM2B	cis	lymphoblastoid	seeQTL
rs9535058	ATAD2	trans	parietal	SCAN
rs9535058	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs9535058	AKAP8L	trans	parietal	SCAN
rs9535058	C13orf1	cis	cerebellum	SCAN
rs9535058	LPAR6	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49193000-49196400	ZNF genes & repeats	Fetal Intestine Small	intestine
2	chr13:49193400-49196200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:49194200-49197200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:49194400-49195000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links