Variant report

Variant	rs9645409
Chromosome Location	chr1:58374317-58374318
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10889075	0.80[CEU][hapmap]
rs11207128	0.80[CEU][hapmap]
rs11207129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12117610	0.80[CEU][hapmap]
rs12402927	0.80[CEU][hapmap]
rs1884487	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6670853	0.80[CEU][hapmap]
rs6679454	0.80[CEU][hapmap]
rs6698981	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58362000-58376400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:58372200-58376600	Enhancers	Fetal Brain Male	brain
3	chr1:58373200-58375000	Enhancers	Fetal Lung	lung
4	chr1:58373600-58376200	Enhancers	Fetal Brain Female	brain
5	chr1:58373800-58374600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:58373800-58374600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr1:58373800-58377400	Enhancers	Brain Germinal Matrix	brain
8	chr1:58374000-58374400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr1:58374000-58374600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:58374200-58374400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:58374200-58374600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:58374200-58374600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:58374200-58374600	Enhancers	Fetal Stomach	stomach

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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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