Variant report

Variant	rs62230464
Chromosome Location	chr3:24535101-24535102
allele	A/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	POLR2A	chr3:24534949-24535129	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:24534554-24538147	PBDE	blood:	n/a	n/a
3	STAT3	chr3:24534931-24535131	MCF10A-Er-Src	breast:	n/a	n/a
4	MYC	chr3:24534748-24535127	MCF10A-Er-Src	breast:	n/a	n/a
5	ARID3A	chr3:24534654-24536907	HepG2	liver:	n/a	n/a
6	E2F4	chr3:24534850-24535150	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23846193..23848940-chr3:24535065..24537255,2	K562	blood:
2	chr3:24313227..24314767-chr3:24532940..24535103,2	MCF-7	breast:
3	chr3:23958569..23960911-chr3:24534140..24537048,3	MCF-7	breast:
4	chr3:24534533..24538643-chr3:24561395..24564731,10	MCF-7	breast:
5	chr3:24534014..24541118-chr3:24556364..24565705,22	MCF-7	breast:

Variant related genes	Relation type
THRB-AS1	TF binding region
ENSG00000174748	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000265028	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs62228829	1.00[AMR][1000 genomes]
rs62228850	1.00[AMR][1000 genomes]
rs62228853	1.00[AMR][1000 genomes]
rs62228855	1.00[AMR][1000 genomes]
rs62228856	1.00[AMR][1000 genomes]
rs62228859	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62230460	1.00[AMR][1000 genomes]
rs62230461	0.98[EUR][1000 genomes]
rs62230463	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs721216	1.00[AMR][1000 genomes]
rs73036459	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73036460	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1012975	chr3:24500706-24615644	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv999384	chr3:24525345-24656873	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24527600-24535400	Weak transcription	Lung	lung
2	chr3:24529800-24535200	Weak transcription	NHEK	skin
3	chr3:24532200-24535200	Weak transcription	Right Atrium	heart
4	chr3:24532200-24535400	Weak transcription	Pancreas	Pancrea
5	chr3:24533400-24535200	Weak transcription	Left Ventricle	heart
6	chr3:24533600-24535400	Active TSS	Fetal Intestine Large	intestine
7	chr3:24533600-24535600	Active TSS	Fetal Intestine Small	intestine
8	chr3:24533600-24537200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:24533600-24537800	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr3:24533800-24535200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:24533800-24535200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:24533800-24535400	Weak transcription	Esophagus	oesophagus
13	chr3:24533800-24535400	Bivalent/Poised TSS	Fetal Brain Male	brain
14	chr3:24533800-24535400	Bivalent/Poised TSS	Fetal Brain Female	brain
15	chr3:24533800-24535400	Weak transcription	Gastric	stomach
16	chr3:24533800-24537000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
17	chr3:24533800-24537400	Active TSS	Brain Angular Gyrus	brain
18	chr3:24534000-24535200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:24534000-24535200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr3:24534000-24537000	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr3:24534000-24537000	Active TSS	Stomach Smooth Muscle	stomach
22	chr3:24534200-24537000	Active TSS	Liver	Liver
23	chr3:24534400-24535200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr3:24534400-24535400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
25	chr3:24534400-24537000	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr3:24534400-24538200	Active TSS	Aorta	Aorta
27	chr3:24534600-24535200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
28	chr3:24534600-24535200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:24534600-24535200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:24534600-24535200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr3:24534600-24535200	Enhancers	Brain Substantia Nigra	brain
32	chr3:24534600-24535200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr3:24534600-24535200	Active TSS	Fetal Stomach	stomach
34	chr3:24534600-24535200	Flanking Active TSS	NHDF-Ad	bronchial
35	chr3:24534600-24535400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr3:24534600-24535800	Bivalent/Poised TSS	Fetal Kidney	kidney
37	chr3:24534600-24537200	Active TSS	Psoas Muscle	Psoas
38	chr3:24534600-24537400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr3:24534600-24537600	Active TSS	Brain Anterior Caudate	brain
40	chr3:24534600-24537600	Active TSS	Brain Cingulate Gyrus	brain
41	chr3:24534800-24535200	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
42	chr3:24534800-24535200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:24534800-24535200	Flanking Active TSS	HMEC	breast
44	chr3:24534800-24535200	Active TSS	K562	blood
45	chr3:24534800-24535400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
46	chr3:24534800-24535400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
47	chr3:24534800-24536400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:24534800-24537200	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr3:24534800-24537400	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr3:24534800-24537400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links