Variant report

Variant	rs1573497
Chromosome Location	chr18:39675052-39675053
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10221315	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10468957	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11082255	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs11659568	0.93[ASN][1000 genomes]
rs11660388	0.93[ASN][1000 genomes]
rs11660513	0.93[ASN][1000 genomes]
rs12326267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12327365	0.93[ASN][1000 genomes]
rs12455083	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12456084	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12456573	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12456934	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12457082	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12457086	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12457525	0.80[EUR][1000 genomes]
rs12954202	0.92[ASN][1000 genomes]
rs12964834	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12964931	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12966303	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1557418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557419	0.93[ASN][1000 genomes]
rs1941526	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1941532	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1984366	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1984367	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2096896	0.93[ASN][1000 genomes]
rs2096897	0.93[ASN][1000 genomes]
rs2105680	0.93[ASN][1000 genomes]
rs2156015	0.81[EUR][1000 genomes]
rs34966612	0.80[EUR][1000 genomes]
rs3932738	0.93[ASN][1000 genomes]
rs3932739	0.93[ASN][1000 genomes]
rs4121647	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4121811	0.92[ASN][1000 genomes]
rs4890222	0.87[ASN][1000 genomes]
rs4890377	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[YRI][hapmap]
rs4890379	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5004531	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs536139	0.93[ASN][1000 genomes]
rs56147258	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569983	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs581950	0.94[CEU][hapmap];0.91[CHB][hapmap]
rs60861018	0.83[EUR][1000 genomes]
rs61107251	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62082282	0.80[EUR][1000 genomes]
rs62082880	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62082911	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs627099	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs650586	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs657164	0.94[CEU][hapmap];0.87[CHB][hapmap]
rs667503	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs66960332	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7237998	0.86[ASN][1000 genomes]
rs7504589	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8093251	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs948871	0.93[ASN][1000 genomes]
rs948872	0.92[ASN][1000 genomes]
rs948873	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9635942	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9807114	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9989595	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv1057988	chr18:39618253-39713904	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1065792	chr18:39619676-39711798	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
10	nsv1057790	chr18:39621947-39705550	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
11	esv2762006	chr18:39621947-39713916	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
12	nsv1063952	chr18:39621947-39718600	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
13	nsv1064973	chr18:39623604-39711798	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv833631	chr18:39633503-39824091	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1573497	CELF4	cis	cerebellum	SCAN
rs1573497	PIK3C3	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39653000-39683400	Weak transcription	Aorta	Aorta
2	chr18:39659800-39675400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr18:39663200-39675400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr18:39674400-39676800	Enhancers	Fetal Intestine Large	intestine
5	chr18:39674600-39675800	Enhancers	Fetal Intestine Small	intestine
6	chr18:39675000-39676600	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links