Variant report

Variant	rs9289185
Chromosome Location	chr3:121705900-121705901
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10934568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs11916150	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12489511	0.86[GIH][hapmap]
rs12490565	0.82[CHB][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap]
rs12695420	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13068522	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1474327	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1589700	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2091665	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2141614	0.81[JPT][hapmap]
rs2332056	0.90[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.87[TSI][hapmap]
rs2700424	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3817599	0.84[CEU][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4419417	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438689	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6770115	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6770719	0.86[GIH][hapmap];0.81[JPT][hapmap]
rs6780559	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7626740	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628167	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7638094	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646346	0.82[CHB][hapmap]
rs7647751	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289184	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs953730	0.88[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9815649	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9828757	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9829181	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9843053	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9289185	SLC15A2	cis	parietal	SCAN
rs9289185	SLC15A2	cis	cerebellum	SCAN
rs9289185	HCLS1	cis	multi-tissue	Pritchard
rs9289185	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs9289185	CCDC14	cis	cerebellum	SCAN
rs9289185	MUC13	cis	cerebellum	SCAN
rs9289185	ADPRH	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121699000-121711200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:121699400-121714200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:121702600-121711600	Weak transcription	Fetal Intestine Small	intestine
4	chr3:121703000-121709000	Weak transcription	Fetal Intestine Large	intestine
5	chr3:121703200-121709000	Weak transcription	Primary B cells from cord blood	blood
6	chr3:121703400-121706400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:121703600-121707400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:121704200-121708800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr3:121704200-121709000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr3:121704800-121706800	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr3:121704800-121721400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:121705000-121711600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:121705200-121707400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:121705200-121714000	Weak transcription	HMEC	breast
15	chr3:121705200-121729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:121705400-121706000	Weak transcription	GM12878-XiMat	blood

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