Variant report

Variant	rs73173989
Chromosome Location	chr5:89827380-89827381
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr5:89827219-89827489	K562	blood:	n/a	n/a
2	NFIC	chr5:89826857-89827423	ECC-1	luminal epithelium:	n/a	chr5:89827092-89827109 chr5:89827092-89827108
3	GATA3	chr5:89827286-89827627	T-47D	breast:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:89826684..89828882-chr5:89853247..89854802,2	K562	blood:
2	chr5:89825930..89827528-chr5:89867274..89868949,2	MCF-7	breast:
3	chr5:89825899..89828736-chr5:89905925..89909224,3	K562	blood:
4	chr5:89825541..89827508-chr5:89852797..89855537,2	MCF-7	breast:
5	chr5:89708413..89711602-chr5:89825612..89828655,3	K562	blood:
6	chr5:89766469..89774126-chr5:89823341..89829105,11	K562	blood:
7	chr5:89826971..89828828-chr5:89846994..89849813,2	MCF-7	breast:
8	chr5:89826199..89831045-chr5:89834037..89838315,7	K562	blood:
9	chr5:89825598..89829055-chr5:89851441..89854747,4	K562	blood:
10	chr5:89768855..89773751-chr5:89822671..89829297,12	K562	blood:
11	chr5:89767818..89772796-chr5:89823286..89827702,11	MCF-7	breast:

No data

Variant related genes	Relation type
LYSMD3	TF binding region
ENSG00000113356	Chromatin interaction
ENSG00000176055	Chromatin interaction
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs56983849	1.00[EUR][1000 genomes]
rs57242895	1.00[EUR][1000 genomes]
rs57287532	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58741440	1.00[EUR][1000 genomes]
rs58953839	1.00[EUR][1000 genomes]
rs61201553	1.00[EUR][1000 genomes]
rs6452892	1.00[EUR][1000 genomes]
rs73176094	1.00[EUR][1000 genomes]
rs73176098	1.00[EUR][1000 genomes]
rs73177824	1.00[EUR][1000 genomes]
rs73177840	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73179713	1.00[EUR][1000 genomes]
rs73181603	0.86[AFR][1000 genomes]
rs73181619	0.86[AFR][1000 genomes]
rs73181634	1.00[AFR][1000 genomes]
rs73181640	1.00[AFR][1000 genomes]
rs73181642	0.83[AFR][1000 genomes]
rs7724507	1.00[EUR][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	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv882366	chr5:89826726-89894564	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 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	chr5:89826200-89827400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:89826200-89842800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:89826400-89827400	Enhancers	Brain Substantia Nigra	brain
4	chr5:89826600-89827400	Enhancers	NH-A	brain
5	chr5:89826600-89827600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:89826600-89831000	Weak transcription	Fetal Intestine Small	intestine
7	chr5:89826600-89831200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:89826600-89833000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:89826600-89833400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:89826800-89827400	Active TSS	Brain Angular Gyrus	brain
11	chr5:89826800-89827400	Enhancers	Brain Hippocampus Middle	brain
12	chr5:89826800-89843200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr5:89827000-89827400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:89827000-89827400	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr5:89827000-89829600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:89827000-89829800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:89827200-89827400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr5:89827200-89827400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:89827200-89827400	Bivalent Enhancer	Fetal Kidney	kidney
20	chr5:89827200-89827400	Enhancers	K562	blood
21	chr5:89827200-89829200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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