Variant report

Variant	rs40603
Chromosome Location	chr5:88564391-88564392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2545606	0.82[ASN][1000 genomes]
rs2561590	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41134	0.85[ASN][1000 genomes]
rs62378213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs771438	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv532159	chr5:88016214-88783092	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv533373	chr5:88062497-89028098	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv532160	chr5:88150666-88564477	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv529543	chr5:88348147-88783092	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv830387	chr5:88547862-88682442	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:88561400-88575400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:88562000-88564400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:88562000-88566600	Weak transcription	HSMMtube	muscle
4	chr5:88562000-88567000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr5:88562200-88566600	Weak transcription	HSMM	muscle
6	chr5:88562400-88571800	Enhancers	Primary B cells from peripheral blood	blood
7	chr5:88562600-88565200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr5:88562600-88567000	Enhancers	Primary B cells from cord blood	blood
9	chr5:88562600-88569400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr5:88562800-88568200	Enhancers	Primary hematopoietic stem cells	blood
11	chr5:88562800-88569400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:88563800-88564600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr5:88564000-88564400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:88564000-88564600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:88564000-88565000	Flanking Active TSS	GM12878-XiMat	blood
16	chr5:88564200-88564600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:88564200-88564800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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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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