Variant report

Variant	rs1741797
Chromosome Location	chr6:64058565-64058566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:64057634..64059161-chr6:64281523..64283392,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266680	Chromatin interaction
ENSG00000112245	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs1614600	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][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	nsv1019831	chr6:63279677-64230736	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv538270	chr6:63682752-64147241	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1031548	chr6:64026862-64102045	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1030651	chr6:64028392-64102045	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1741797	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64040400-64071200	Weak transcription	Placenta	Placenta
2	chr6:64056600-64059800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:64056800-64059600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:64057000-64059200	Enhancers	NHEK	skin
5	chr6:64057000-64059600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:64057000-64059800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr6:64057200-64059000	Enhancers	HMEC	breast
8	chr6:64057200-64059800	Enhancers	NHDF-Ad	bronchial
9	chr6:64057200-64060000	Enhancers	HUVEC	blood vessel
10	chr6:64057200-64062200	Enhancers	Hela-S3	cervix
11	chr6:64057400-64059200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:64058000-64059000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:64058000-64059400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr6:64058000-64059400	Enhancers	Stomach Mucosa	stomach
15	chr6:64058000-64062200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:64058200-64058600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:64058200-64058600	Weak transcription	Osteobl	bone
18	chr6:64058200-64060000	Enhancers	Fetal Intestine Small	intestine
19	chr6:64058200-64061200	Enhancers	Fetal Intestine Large	intestine
20	chr6:64058200-64062000	Weak transcription	HepG2	liver
21	chr6:64058400-64058800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:64058400-64058800	Weak transcription	A549	lung
23	chr6:64058400-64062000	Weak transcription	NHLF	lung

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