Variant report

Variant	rs9962333
Chromosome Location	chr18:29076829-29076830
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:28680816..28682711-chr18:29076315..29078384,2	K562	blood:

Variant related genes	Relation type
ENSG00000265888	Chromatin interaction
ENSG00000134755	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1031729	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11081701	0.87[ASN][1000 genomes]
rs1350731	0.83[ASN][1000 genomes]
rs1460602	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17660585	0.88[ASN][1000 genomes]
rs1824477	0.81[ASN][1000 genomes]
rs1841396	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2212617	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2212618	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2219584	0.83[ASN][1000 genomes]
rs2704050	0.82[ASN][1000 genomes]
rs2704051	0.84[ASN][1000 genomes]
rs2704052	0.85[ASN][1000 genomes]
rs2704053	0.85[ASN][1000 genomes]
rs2704055	0.98[ASN][1000 genomes]
rs2848677	0.85[ASN][1000 genomes]
rs2848680	0.85[ASN][1000 genomes]
rs2848681	0.85[ASN][1000 genomes]
rs4799310	0.88[ASN][1000 genomes]
rs4799573	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6506927	0.83[ASN][1000 genomes]
rs6506928	0.83[ASN][1000 genomes]
rs7227343	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7227984	0.88[ASN][1000 genomes]
rs7231288	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7231553	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7232282	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7235272	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7236324	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7236469	0.88[ASN][1000 genomes]
rs7238729	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7240824	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7240920	0.82[EUR][1000 genomes]
rs7241107	0.81[ASN][1000 genomes]
rs73414280	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73953901	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9304097	0.83[ASN][1000 genomes]
rs9304098	0.98[ASN][1000 genomes]
rs9304099	0.88[ASN][1000 genomes]
rs9941421	0.81[ASN][1000 genomes]
rs9945031	0.88[ASN][1000 genomes]
rs9945420	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9951843	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9961910	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9961920	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9961925	0.88[ASN][1000 genomes]
rs9962121	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9962318	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9962423	0.88[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	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9962333	RP11-650P15.1	cis	Thyroid	GTEx
rs9962333	DSG2	Cis_1M	lymphoblastoid	RTeQTL
rs9962333	RP11-650P15.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29071200-29077200	Weak transcription	Fetal Intestine Small	intestine
2	chr18:29071800-29077400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr18:29071800-29077400	Weak transcription	HMEC	breast
4	chr18:29072000-29077200	Weak transcription	NHEK	skin
5	chr18:29072000-29077400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr18:29072200-29077600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr18:29074200-29077200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr18:29074400-29077400	Weak transcription	GM12878-XiMat	blood
9	chr18:29074800-29077400	Weak transcription	Colonic Mucosa	Colon
10	chr18:29075200-29077200	Weak transcription	K562	blood
11	chr18:29076800-29077200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr18:29076800-29077200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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