Variant report

Variant	rs60252299
Chromosome Location	chr4:7948064-7948065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:7939921..7943801-chr4:7946020..7949690,5	MCF-7	breast:
2	chr4:7946085..7948166-chr4:7952831..7955364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228919	Chromatin interaction
ENSG00000196526	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs56125412	1.00[AMR][1000 genomes]
rs58156060	1.00[AMR][1000 genomes]
rs58161931	1.00[AMR][1000 genomes]
rs73795054	1.00[AMR][1000 genomes]
rs73795057	1.00[AMR][1000 genomes]
rs73795747	1.00[AMR][1000 genomes]
rs73798024	1.00[AMR][1000 genomes]
rs73798025	1.00[AMR][1000 genomes]
rs73798048	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv878578	chr4:7841833-7969594	Enhancers Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv593621	chr4:7943106-7969594	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7941600-7951200	Weak transcription	Small Intestine	intestine
2	chr4:7942000-7950400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:7942000-7951000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:7942000-7951400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:7942200-7950600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:7943600-7950600	Weak transcription	Fetal Heart	heart
7	chr4:7945400-7957400	Weak transcription	Placenta	Placenta
8	chr4:7946200-7948400	Enhancers	Fetal Intestine Small	intestine
9	chr4:7946400-7948200	Enhancers	Fetal Stomach	stomach
10	chr4:7946600-7948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:7946800-7948200	Enhancers	HepG2	liver
12	chr4:7946800-7950800	Weak transcription	Liver	Liver
13	chr4:7947200-7948200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:7947400-7948200	Enhancers	Pancreas	Pancrea
15	chr4:7947400-7948400	Enhancers	Fetal Brain Male	brain
16	chr4:7947400-7948400	Enhancers	Fetal Brain Female	brain
17	chr4:7947600-7948200	Enhancers	Fetal Lung	lung
18	chr4:7947600-7948400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr4:7947600-7948400	Enhancers	Fetal Muscle Leg	muscle
20	chr4:7947600-7950400	Weak transcription	Fetal Intestine Large	intestine
21	chr4:7947800-7948200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:7947800-7948400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:7947800-7948400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr4:7947800-7948400	Enhancers	Ovary	ovary
25	chr4:7947800-7948600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:7948000-7948200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:7948000-7948200	Enhancers	Fetal Kidney	kidney
28	chr4:7948000-7950600	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links