Variant report

Variant	rs58043268
Chromosome Location	chr2:134329102-134329103
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	RAD21	chr2:134328805-134329179	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr2:134328791-134329161	H1-hESC	embryonic stem cell:	n/a	n/a
3	E2F6	chr2:134328816-134329276	H1-hESC	embryonic stem cell:	n/a	chr2:134329031-134329040
4	SP1	chr2:134328706-134329107	H1-hESC	embryonic stem cell:	n/a	chr2:134328930-134328944 chr2:134328939-134328950 chr2:134329030-134329039 chr2:134328927-134328938 chr2:134329030-134329044 chr2:134329031-134329040

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:134325568..134327875-chr2:134328261..134331038,2	MCF-7	breast:

Variant related genes	Relation type
NCKAP5	TF binding region
ENSG00000176771	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16826544	0.80[AFR][1000 genomes]
rs57893181	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59731226	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72994270	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs72994274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72994291	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72994298	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72996109	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1003624	chr2:134126928-134583203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1006101	chr2:134263288-134973917	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv516644	chr2:134301130-134391214	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv431713	chr2:134316522-134413604	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1013713	chr2:134322236-134644574	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv535931	chr2:134322236-134644574	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134324600-134329600	Enhancers	H1 Cell Line	embryonic stem cell
2	chr2:134324600-134330400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:134325000-134330000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:134325000-134342400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:134325400-134331800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:134326200-134329600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:134326200-134329800	Weak transcription	Esophagus	oesophagus
8	chr2:134326200-134337000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr2:134326400-134329800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:134326400-134330400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:134326400-134331800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:134326400-134331800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:134326400-134332400	Weak transcription	Right Atrium	heart
14	chr2:134326400-134334200	Weak transcription	Liver	Liver
15	chr2:134326400-134336200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:134326400-134337000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:134326600-134331000	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:134326600-134331800	Weak transcription	HUVEC	blood vessel
19	chr2:134326600-134334000	Weak transcription	NHEK	skin
20	chr2:134326600-134334200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:134326600-134334600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:134326600-134336000	Weak transcription	Brain Anterior Caudate	brain
23	chr2:134326600-134344200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:134326800-134332400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:134327200-134331000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:134327200-134331400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:134327200-134331800	Weak transcription	Brain Substantia Nigra	brain
28	chr2:134327200-134332400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:134327400-134331800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:134327400-134332000	Weak transcription	NH-A	brain
31	chr2:134327600-134331000	Weak transcription	Fetal Heart	heart
32	chr2:134328000-134330200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr2:134328200-134329200	Enhancers	Fetal Intestine Large	intestine
34	chr2:134328200-134330000	Enhancers	H9 Cell Line	embryonic stem cell
35	chr2:134328400-134330200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr2:134328600-134329200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr2:134328800-134329200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:134328800-134329400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:134329000-134329400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr2:134329000-134329400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:134329000-134329400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr2:134329000-134329400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr2:134329000-134330000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr2:134329000-134330200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr2:134329000-134331800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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