Variant report

Variant	rs1494857
Chromosome Location	chr1:79960198-79960199
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10493629	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11588913	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12727530	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12727721	0.84[AMR][1000 genomes]
rs12739748	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12739762	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1353290	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1389940	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389942	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1389943	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389944	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389946	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1389947	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1494843	0.82[AMR][1000 genomes]
rs1494856	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17418579	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17453037	0.85[AMR][1000 genomes]
rs1994938	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029788	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2101800	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2132055	0.82[AMR][1000 genomes]
rs2132057	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2860503	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2934867	0.84[AMR][1000 genomes]
rs2934868	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2934871	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2934873	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2934878	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3000098	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3000101	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3000110	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3000133	0.80[EUR][1000 genomes]
rs3000142	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3000148	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3000155	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3000174	0.83[EUR][1000 genomes]
rs3000175	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3000176	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3000177	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3000179	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3015006	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3015008	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3015013	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3015014	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3015017	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3015019	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015021	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3015022	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3015025	0.80[EUR][1000 genomes]
rs3015107	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3122389	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34322872	0.83[AMR][1000 genomes]
rs35624469	0.85[AMR][1000 genomes]
rs35938583	0.84[AMR][1000 genomes]
rs4506421	0.85[AMR][1000 genomes]
rs4604653	0.80[AMR][1000 genomes]
rs58635031	0.84[AMR][1000 genomes]
rs59395170	0.86[AMR][1000 genomes]
rs61031256	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004014	chr1:79811049-80042309	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1012004	chr1:79945395-80096748	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv535017	chr1:79945395-80096748	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1012296	chr1:79945395-80300216	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1005022	chr1:79950774-80106902	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1494857	USP33	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79951600-79960400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:79958800-79960200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:79959200-79960600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr1:79959600-79962200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:79959800-79961400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:79960000-79960400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:79960000-79960600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr1:79960000-79960600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:79960000-79960600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:79960000-79963200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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