Variant report

Variant	rs61753342
Chromosome Location	chr4:106473983-106473984
allele	C/T
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	POLR2A	chr4:106473925-106473995	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr4:106472945-106474009	T-47D	breast:	n/a	n/a
3	GATA3	chr4:106473093-106474008	T-47D	breast:	n/a	n/a
4	EP300	chr4:106472872-106473985	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106473010..106475476-chr4:106482085..106484725,2	MCF-7	breast:
2	chr4:106452636..106454650-chr4:106472579..106474364,2	MCF-7	breast:

Variant related genes	Relation type
ARHGEF38	TF binding region
ENSG00000250522	TF binding region
ENSG00000250922	Chromatin interaction
ENSG00000249885	Chromatin interaction

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

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

rs_ID	r²[population]
rs17035732	1.00[AMR][1000 genomes]
rs17035801	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6849578	1.00[AMR][1000 genomes]
rs7679119	1.00[AMR][1000 genomes]
rs7699857	1.00[AMR][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	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv1005011	chr4:106461690-106496019	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1013019	chr4:106461690-106501412	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv524424	chr4:106466128-106491511	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv461610	chr4:106466128-106491511	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv595008	chr4:106466128-106491511	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv517837	chr4:106466588-106502513	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106470000-106476600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:106471400-106474200	Enhancers	HMEC	breast
3	chr4:106471600-106474000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:106471600-106474200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:106471600-106474200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:106471800-106474200	Enhancers	NHEK	skin
7	chr4:106472200-106477600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr4:106472800-106474600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:106472800-106474800	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr4:106473000-106474000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:106473000-106474600	Active TSS	Colonic Mucosa	Colon
12	chr4:106473000-106475400	Active TSS	Pancreas	Pancrea
13	chr4:106473200-106474000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
14	chr4:106473200-106474000	Active TSS	Fetal Lung	lung
15	chr4:106473200-106474000	Enhancers	Fetal Thymus	thymus
16	chr4:106473200-106474200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:106473200-106474200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr4:106473200-106474200	Enhancers	Placenta	Placenta
19	chr4:106473200-106474600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
20	chr4:106473200-106474600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
21	chr4:106473200-106475000	Active TSS	Rectal Smooth Muscle	rectum
22	chr4:106473400-106474000	Enhancers	Primary hematopoietic stem cells	blood
23	chr4:106473400-106474000	Enhancers	Esophagus	oesophagus
24	chr4:106473400-106474000	Flanking Active TSS	Fetal Kidney	kidney
25	chr4:106473400-106474200	ZNF genes & repeats	Lung	lung
26	chr4:106473400-106474800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:106473400-106475200	Active TSS	Fetal Stomach	stomach
28	chr4:106473400-106476400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:106473600-106474000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:106473600-106474000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:106473600-106474200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:106473600-106474200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:106473600-106474400	Active TSS	Stomach Mucosa	stomach
34	chr4:106473600-106475600	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr4:106473600-106477400	Active TSS	Duodenum Mucosa	Duodenum
36	chr4:106473600-106477600	Active TSS	Fetal Intestine Large	intestine
37	chr4:106473600-106477600	Weak transcription	Gastric	stomach
38	chr4:106473800-106474000	Flanking Active TSS	Fetal Intestine Small	intestine
39	chr4:106473800-106474200	Active TSS	Sigmoid Colon	Sigmoid Colon
40	chr4:106473800-106474400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
41	chr4:106473800-106474800	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr4:106473800-106476200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links