Variant report

Variant	rs598098
Chromosome Location	chr1:179900112-179900113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179899957..179900671-chr1:180137065..180137612,2	MCF-7	breast:
2	chr1:179894610..179897527-chr1:179897909..179900887,3	MCF-7	breast:
3	chr1:179899158..179900985-chr1:184603757..184605765,2	MCF-7	breast:
4	chr1:179893782..179897328-chr1:179897862..179901956,4	MCF-7	breast:
5	chr1:179889909..179891977-chr1:179899561..179901875,2	K562	blood:
6	chr1:179898810..179900378-chr1:179923745..179926057,2	MCF-7	breast:
7	chr1:179899316..179902029-chr1:179921457..179922978,2	MCF-7	breast:
8	chr1:179898573..179901417-chr1:179902522..179905124,2	MCF-7	breast:
9	chr1:179899680..179902372-chr1:179905754..179907325,2	K562	blood:
10	chr1:179898424..179901062-chr1:179905240..179907123,2	MCF-7	breast:
11	chr1:179899505..179902382-chr1:179923017..179925632,3	MCF-7	breast:
12	chr1:179850492..179853577-chr1:179898721..179902201,5	MCF-7	breast:

No data

No data

No data

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs507603	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs530369	0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs539181	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555526	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs585355	0.85[CEU][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs598098	FAM5B	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179887400-179900600	Weak transcription	Ovary	ovary
2	chr1:179887400-179901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:179888800-179900600	Weak transcription	Adipose Nuclei	Adipose
4	chr1:179896200-179900200	Weak transcription	NHEK	skin
5	chr1:179897600-179900600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:179898600-179902200	Enhancers	Fetal Intestine Large	intestine
7	chr1:179899200-179900200	Enhancers	Osteobl	bone
8	chr1:179899200-179901400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:179899400-179900200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:179899400-179900400	Enhancers	K562	blood
11	chr1:179899400-179900800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:179899400-179901200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:179899400-179901200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:179899600-179901400	Enhancers	Duodenum Mucosa	Duodenum
15	chr1:179899600-179905000	Weak transcription	GM12878-XiMat	blood
16	chr1:179899800-179900600	Weak transcription	Stomach Mucosa	stomach
17	chr1:179899800-179901000	Weak transcription	Small Intestine	intestine
18	chr1:179899800-179902200	Enhancers	Hela-S3	cervix

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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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