Variant report

Variant	rs4683799
Chromosome Location	chr3:139210258-139210259
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	FOXA1	chr3:139210203-139210422	T-47D	breast:	n/a	n/a
2	FOXA1	chr3:139210142-139210408	HepG2	liver:	n/a	n/a
3	FOXA1	chr3:139210132-139210472	HepG2	liver:	n/a	n/a
4	TCF12	chr3:139210140-139210462	H1-hESC	embryonic stem cell:	n/a	n/a
5	FOXA2	chr3:139210229-139210487	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000263538	TF binding region
ACTG1P1	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12494556	0.88[EUR][1000 genomes]
rs12695700	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13071857	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13074208	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13086868	0.87[EUR][1000 genomes]
rs13089052	0.88[EUR][1000 genomes]
rs167184	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4683818	0.87[EUR][1000 genomes]
rs747346	0.89[EUR][1000 genomes]
rs9834607	0.89[EUR][1000 genomes]
rs9835241	0.89[EUR][1000 genomes]
rs9860521	0.88[EUR][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	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1001460	chr3:139194633-139241616	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139208000-139215400	Weak transcription	Fetal Kidney	kidney
2	chr3:139208200-139249600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:139209200-139213000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:139209800-139210400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:139209800-139210400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:139209800-139210600	Enhancers	HMEC	breast
7	chr3:139210000-139210400	Enhancers	Duodenum Mucosa	Duodenum
8	chr3:139210000-139210400	Enhancers	NHEK	skin
9	chr3:139210000-139210600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:139210000-139210600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:139210000-139210800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:139210000-139210800	Enhancers	Fetal Intestine Large	intestine
13	chr3:139210000-139210800	Enhancers	Fetal Intestine Small	intestine
14	chr3:139210000-139211400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:139210000-139211600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr3:139210200-139210400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr3:139210200-139210400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:139210200-139210400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:139210200-139210400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr3:139210200-139210400	Enhancers	Esophagus	oesophagus
21	chr3:139210200-139210400	Enhancers	Fetal Stomach	stomach
22	chr3:139210200-139210400	Enhancers	Stomach Smooth Muscle	stomach
23	chr3:139210200-139210600	Enhancers	Right Atrium	heart
24	chr3:139210200-139211000	Enhancers	Pancreas	Pancrea
25	chr3:139210200-139211200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:139210200-139211200	Enhancers	Left Ventricle	heart
27	chr3:139210200-139211400	Enhancers	H9 Cell Line	embryonic stem cell
28	chr3:139210200-139211400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr3:139210200-139212600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:139210200-139212800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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