Variant report

Variant	rs1416341
Chromosome Location	chr1:58621964-58621965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10493244	0.84[CEU][hapmap]
rs11799299	0.84[CEU][hapmap]
rs11802821	0.84[CEU][hapmap];0.83[TSI][hapmap]
rs12025945	1.00[ASN][1000 genomes]
rs12034198	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040062	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12042276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12048970	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs12565597	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13374932	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs1342875	0.84[CEU][hapmap]
rs1416343	0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1416346	0.84[CEU][hapmap]
rs1418765	1.00[ASN][1000 genomes]
rs17116983	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs17116988	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs17117013	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs17117039	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs17117101	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs1776192	0.83[CEU][hapmap]
rs1832489	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs1953811	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs2225949	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs2406591	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2797608	0.82[CEU][hapmap]
rs3850534	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3850535	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs3905539	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs6667829	0.93[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6701275	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74074998	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7551611	0.84[CEU][hapmap]

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	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1416341	DAB1	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58619800-58622200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:58620000-58622600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:58620200-58622000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:58620800-58622200	Weak transcription	Left Ventricle	heart
5	chr1:58620800-58623000	Enhancers	Fetal Heart	heart
6	chr1:58620800-58623400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr1:58620800-58625200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr1:58621000-58622000	Enhancers	Liver	Liver
9	chr1:58621000-58622200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:58621000-58622400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:58621200-58623000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:58621200-58624200	Weak transcription	Thymus	Thymus
13	chr1:58621200-58625200	Enhancers	GM12878-XiMat	blood
14	chr1:58621200-58626400	Enhancers	Fetal Thymus	thymus
15	chr1:58621200-58626800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:58621200-58629400	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr1:58621400-58622400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:58621400-58624600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr1:58621600-58623200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:58621800-58622200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:58621800-58622800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:58621800-58623200	Weak transcription	Fetal Brain Male	brain

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