Variant report

Variant	rs2145403
Chromosome Location	chr1:57315032-57315033
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1033637	0.83[AFR][1000 genomes]
rs10489624	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs592451	0.83[CHB][hapmap]
rs594105	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs607221	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs618707	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs621819	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs622300	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs645846	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs652785	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs658461	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs663352	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs668822	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs669444	0.84[AFR][1000 genomes]
rs6696924	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs671137	0.83[AFR][1000 genomes]
rs679350	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs694090	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs880657	0.87[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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1000266	chr1:57291371-57319480	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57310600-57315200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:57310800-57315200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr1:57311000-57315600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:57311200-57315800	Weak transcription	Fetal Brain Female	brain
5	chr1:57311600-57315600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:57311600-57315800	Weak transcription	HepG2	liver
7	chr1:57314400-57317400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:57314600-57317000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:57314800-57316400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:57315000-57315200	Enhancers	Lung	lung
11	chr1:57315000-57316000	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr1:57315000-57316200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:57315000-57316400	Enhancers	HUES48 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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