Variant report

Variant	rs55925475
Chromosome Location	chr5:177778998-177778999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64969090..64970821-chr5:177778955..177780631,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HNRNPAB-3	chr5:177778919-177779251	ENSG00000253698.1

Variant related genes	Relation type
ENSG00000089775	Chromatin interaction
ENSG00000126804	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10059293	0.85[EUR][1000 genomes]
rs55698123	0.85[EUR][1000 genomes]
rs55804624	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55824148	0.85[EUR][1000 genomes]
rs56234995	0.85[EUR][1000 genomes]
rs56366317	0.85[EUR][1000 genomes]
rs56389033	0.85[EUR][1000 genomes]
rs56411453	0.85[EUR][1000 genomes]
rs73346819	0.85[EUR][1000 genomes]
rs73346820	0.85[EUR][1000 genomes]
rs73346822	0.85[EUR][1000 genomes]
rs73346873	0.85[EUR][1000 genomes]
rs73804796	0.85[EUR][1000 genomes]
rs73804801	0.85[EUR][1000 genomes]
rs7725724	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
5	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv883206	chr5:177684682-177796121	Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1027165	chr5:177693601-177843314	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177759400-177783400	Weak transcription	Right Atrium	heart
2	chr5:177768200-177783000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr5:177769600-177783200	Weak transcription	Fetal Thymus	thymus
4	chr5:177775000-177779200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr5:177775400-177779200	Strong transcription	Thymus	Thymus
6	chr5:177776000-177779600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:177776000-177780400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:177776000-177783000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:177776000-177783000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:177776200-177780600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:177776200-177783200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr5:177776200-177783400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:177777200-177779200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:177777400-177780200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:177777800-177783000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:177778000-177783000	Weak transcription	Placenta	Placenta
17	chr5:177778200-177779000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:177778200-177779000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:177778200-177782800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr5:177778400-177779400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr5:177778400-177783000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr5:177778400-177783400	Weak transcription	NHDF-Ad	bronchial
23	chr5:177778600-177779600	Enhancers	Fetal Stomach	stomach
24	chr5:177778600-177781000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:177778600-177782800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:177778600-177783000	Weak transcription	Spleen	Spleen
27	chr5:177778800-177780600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr5:177778800-177783000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:177778800-177783000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links