Variant report

Variant	rs7993248
Chromosome Location	chr13:76255078-76255079
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	chr13:76123564..76125268-chr13:76253504..76256274,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118939	Chromatin interaction
ENSG00000188243	Chromatin interaction
ENSG00000261553	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs7994643	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9544016	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9544018	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9544027	0.87[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751152	chr13:76144199-76288418	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv900579	chr13:76244056-76307981	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7993248	RALGPS2	trans	lymphoblastoid	seeQTL
rs7993248	TBC1D4	cis	lymphoblastoid	seeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76213400-76267800	Weak transcription	Primary T cells from cord blood	blood
2	chr13:76215400-76258200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:76236800-76267600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:76241200-76255600	Weak transcription	HSMMtube	muscle
5	chr13:76249400-76258800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr13:76249800-76258800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:76250000-76258200	Weak transcription	HMEC	breast
8	chr13:76250200-76259000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:76250200-76262800	Weak transcription	Fetal Brain Male	brain
10	chr13:76251000-76256200	Strong transcription	HSMM	muscle
11	chr13:76251400-76256600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr13:76251400-76258800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:76251400-76259600	Weak transcription	Aorta	Aorta
14	chr13:76251600-76259200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr13:76252400-76256200	Strong transcription	Osteobl	bone
16	chr13:76253600-76258800	Weak transcription	NH-A	brain
17	chr13:76253800-76255600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr13:76253800-76259000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:76254000-76257800	Weak transcription	NHLF	lung
20	chr13:76254000-76259200	Weak transcription	HepG2	liver
21	chr13:76254200-76257600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr13:76254200-76258200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr13:76254400-76256200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr13:76254400-76258000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr13:76254400-76258200	Weak transcription	NHDF-Ad	bronchial
26	chr13:76254600-76255600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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