Variant report

Variant	rs1202824
Chromosome Location	chr1:58349005-58349006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1202782	0.93[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1202784	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1202825	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1202827	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1202832	0.90[MEX][hapmap]
rs1202838	0.81[CEU][hapmap]
rs1202844	0.90[MEX][hapmap]
rs1202849	0.81[MEX][hapmap]
rs2038380	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs706412	0.88[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs722187	0.93[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs852792	0.82[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.81[ASN][1000 genomes]
rs852795	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs852798	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs852805	0.88[CEU][hapmap];0.84[CHB][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs852806	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap]
rs852807	0.89[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][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	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	nsv829937	chr1:58258288-58406506	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1008205	chr1:58349005-58375261	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58346000-58349600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:58346800-58349400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:58346800-58350000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:58347400-58349600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:58347800-58359600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:58348200-58353400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:58348800-58349800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:58349000-58349600	Enhancers	Cortex derived primary cultured neurospheres	brain

Quick Search:

Input of quick search could be:

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

what's new

Quick links