Variant report

Variant	rs2004768
Chromosome Location	chr4:8560119-8560120
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:8559980-8560130	GM12872	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8558223..8560238-chr4:8582084..8583922,2	MCF-7	breast:

Variant related genes	Relation type
GPR78	TF binding region
ENSG00000155269	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13116227	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13132489	0.80[ASN][1000 genomes]
rs3103074	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3115384	0.83[ASN][1000 genomes]
rs3115390	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv878612	chr4:8534283-8618916	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv1832730	chr4:8541086-9514568	Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
5	esv1843578	chr4:8541086-9514568	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
6	nsv878613	chr4:8554894-8618916	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv878614	chr4:8554894-8669619	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8549400-8568400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr4:8553800-8560400	Enhancers	Placenta	Placenta
3	chr4:8555200-8562600	Enhancers	Placenta Amnion	Placenta Amnion
4	chr4:8556800-8562000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:8556800-8562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:8557600-8562000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:8558000-8560600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:8558000-8560600	Enhancers	HSMMtube	muscle
9	chr4:8558000-8560800	Enhancers	NHDF-Ad	bronchial
10	chr4:8558200-8560400	Enhancers	HSMM	muscle
11	chr4:8558200-8560800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr4:8558600-8560200	Weak transcription	Osteobl	bone
13	chr4:8559000-8562200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr4:8559200-8562200	Weak transcription	A549	lung
15	chr4:8559800-8560400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:8559800-8560400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:8559800-8560600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:8559800-8560600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr4:8560000-8560600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:8560000-8560600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr4:8560000-8561200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links