Variant report

Variant	rs1335964
Chromosome Location	chr1:216754098-216754099
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10735488	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10735489	0.81[ASN][1000 genomes]
rs10779266	0.85[ASN][1000 genomes]
rs12145069	0.97[ASN][1000 genomes]
rs1391512	0.82[ASW][hapmap];0.88[TSI][hapmap]
rs1419243	0.82[ASW][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs1498277	0.82[YRI][hapmap];0.80[ASN][1000 genomes]
rs1498283	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs1566224	0.82[YRI][hapmap]
rs1817998	0.83[MEX][hapmap];0.88[TSI][hapmap]
rs1819770	0.87[TSI][hapmap]
rs1826977	0.83[MEX][hapmap];0.88[TSI][hapmap]
rs1857403	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1857406	0.80[ASN][1000 genomes]
rs2050526	0.83[MEX][hapmap];0.88[TSI][hapmap]
rs2173374	0.88[TSI][hapmap]
rs2201838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4344380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6604637	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6662267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6673467	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6673703	0.82[ASW][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap]
rs7533007	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes]
rs7535976	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7542567	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.85[ASN][1000 genomes]
rs7550258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549199	chr1:216384908-216814702	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1003815	chr1:216504235-216836498	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv535289	chr1:216504235-216836498	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873178	chr1:216714314-216813244	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv4565	chr1:216720070-216765053	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv468138	chr1:216736138-216762158	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv549203	chr1:216736138-216762158	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1335964	DTL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216721800-216774000	Weak transcription	Placenta	Placenta
2	chr1:216735800-216755000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:216739800-216757200	Weak transcription	Fetal Intestine Large	intestine
4	chr1:216744800-216764600	Weak transcription	Left Ventricle	heart
5	chr1:216750000-216754800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:216750000-216755000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:216750400-216757000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:216752400-216754800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:216754000-216754400	Enhancers	Fetal Lung	lung
10	chr1:216754000-216755200	Enhancers	Fetal Heart	heart

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