Variant report

Variant	rs3788491
Chromosome Location	chr22:33128597-33128598
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11089592	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1894453	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1894454	0.98[ASN][1000 genomes]
rs2008206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2157135	0.84[JPT][hapmap]
rs2157138	0.99[ASN][1000 genomes]
rs2413145	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2413146	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2413147	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788487	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788488	0.83[JPT][hapmap]
rs3788489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788492	0.89[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3788493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3788495	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3788496	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3788497	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3827340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4339044	0.83[JPT][hapmap]
rs4821091	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5754240	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs5994613	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998601	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998602	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5998605	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs5998607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs743739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs762885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606988	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064719	chr22:33028891-33159636	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv588897	chr22:33116314-33139230	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3788491	TMEM163	trans	multi-tissue	Pritchard
rs3788491	LARGE	cis	multi-tissue	Pritchard
rs3788491	TMEM163	cis	Liver	GTEx
rs3788491	FBXO7	cis	multi-tissue	Pritchard
rs3788491	hCT1970729.1	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33120000-33129600	Weak transcription	Right Atrium	heart
2	chr22:33121800-33141400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr22:33127800-33133000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr22:33127800-33133200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr22:33128000-33130400	Weak transcription	Spleen	Spleen
6	chr22:33128200-33129600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr22:33128400-33132200	Enhancers	Thymus	Thymus
8	chr22:33128400-33135000	Enhancers	Fetal Thymus	thymus

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