Variant report

Variant	rs56411453
Chromosome Location	chr5:177759471-177759472
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	chr5:177757932..177760832-chr5:177771910..177774390,2	K562	blood:
2	chr5:177751727..177753386-chr5:177758828..177761752,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10059293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34026456	1.00[AFR][1000 genomes]
rs55698123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55804624	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs55824148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55925475	0.85[EUR][1000 genomes]
rs56234995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56366317	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56389033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73346819	1.00[EUR][1000 genomes]
rs73346820	1.00[EUR][1000 genomes]
rs73346822	1.00[EUR][1000 genomes]
rs73346873	1.00[EUR][1000 genomes]
rs73804796	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73804801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7725724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv883203	chr5:177682664-177766183	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv883205	chr5:177684682-177777888	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv984572	chr5:177737015-177763963	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177749600-177761400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr5:177751400-177759600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:177754000-177759800	Bivalent Enhancer	Fetal Stomach	stomach
4	chr5:177756400-177759800	Enhancers	Placenta	Placenta
5	chr5:177756600-177759800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr5:177756800-177759600	Enhancers	Brain Cingulate Gyrus	brain
7	chr5:177757000-177759600	Enhancers	Brain Hippocampus Middle	brain
8	chr5:177757000-177759600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr5:177757000-177759600	Enhancers	Brain Substantia Nigra	brain
10	chr5:177757200-177759600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:177757200-177759600	Enhancers	Esophagus	oesophagus
12	chr5:177757200-177759800	Enhancers	Fetal Lung	lung
13	chr5:177757400-177762400	Enhancers	Liver	Liver
14	chr5:177757600-177759600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr5:177757600-177759800	Enhancers	Left Ventricle	heart
16	chr5:177757600-177760400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:177757600-177760600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr5:177757600-177760600	Enhancers	Stomach Mucosa	stomach
19	chr5:177757600-177763600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:177757800-177759600	Enhancers	Stomach Smooth Muscle	stomach
21	chr5:177757800-177761400	Enhancers	Gastric	stomach
22	chr5:177758000-177761400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:177758000-177761800	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr5:177758000-177764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:177758200-177759600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:177758200-177759600	Enhancers	Colonic Mucosa	Colon
27	chr5:177758200-177759600	Enhancers	HSMM	muscle
28	chr5:177758200-177759800	Flanking Active TSS	Hela-S3	cervix
29	chr5:177758200-177760800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:177758200-177762200	Weak transcription	Dnd41	blood
31	chr5:177758400-177760800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr5:177758400-177760800	Enhancers	Fetal Heart	heart
33	chr5:177758400-177762200	Weak transcription	Thymus	Thymus
34	chr5:177758600-177759600	Enhancers	Brain Anterior Caudate	brain
35	chr5:177758800-177759800	Enhancers	Colon Smooth Muscle	Colon
36	chr5:177759000-177761400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:177759200-177761400	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:177759200-177761800	Weak transcription	Fetal Thymus	thymus
39	chr5:177759200-177764000	Weak transcription	Brain Germinal Matrix	brain
40	chr5:177759200-177765000	Enhancers	Fetal Muscle Leg	muscle
41	chr5:177759400-177759600	Enhancers	Fetal Kidney	kidney
42	chr5:177759400-177759800	Enhancers	Duodenum Mucosa	Duodenum
43	chr5:177759400-177760000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr5:177759400-177760000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr5:177759400-177760000	Enhancers	HSMMtube	muscle
46	chr5:177759400-177760400	Weak transcription	Lung	lung
47	chr5:177759400-177760400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:177759400-177760400	Weak transcription	Spleen	Spleen
49	chr5:177759400-177760600	Weak transcription	Right Ventricle	heart
50	chr5:177759400-177762000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links