Variant report

Variant	rs10056758
Chromosome Location	chr5:179389836-179389837
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	chr5:179389750-179390073	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179387216..179389943-chr5:179396226..179399664,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249412	TF binding region

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10054685	0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10059710	0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10060093	0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10061208	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10076682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10479552	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11949896	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11958554	1.00[AMR][1000 genomes]
rs11959514	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12332469	0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73344319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179370200-179392800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:179373400-179400600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:179373800-179401600	Weak transcription	Colonic Mucosa	Colon
4	chr5:179375400-179392600	Weak transcription	Fetal Kidney	kidney
5	chr5:179376600-179390000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:179376600-179406600	Weak transcription	Psoas Muscle	Psoas
7	chr5:179379000-179390200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:179380000-179392600	Weak transcription	NH-A	brain
9	chr5:179380000-179410800	Weak transcription	Small Intestine	intestine
10	chr5:179380200-179401200	Weak transcription	Esophagus	oesophagus
11	chr5:179380400-179393600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:179381000-179397000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:179381000-179397200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:179381000-179407800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:179381200-179396600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:179381200-179397200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:179381200-179402200	Weak transcription	Fetal Heart	heart
18	chr5:179381200-179405600	Weak transcription	NHLF	lung
19	chr5:179381400-179390200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr5:179381600-179393600	Weak transcription	Osteobl	bone
21	chr5:179381600-179411800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:179381800-179392600	Weak transcription	HSMM	muscle
23	chr5:179381800-179402200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:179382000-179392600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr5:179382000-179401400	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:179382200-179401400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:179382600-179390400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:179382800-179400600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr5:179383200-179394600	Weak transcription	Stomach Mucosa	stomach
30	chr5:179383200-179408600	Weak transcription	A549	lung
31	chr5:179384000-179394400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:179385200-179397600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:179386000-179401000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr5:179386800-179397600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:179386800-179397600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:179387200-179390400	Genic enhancers	Brain Hippocampus Middle	brain
37	chr5:179387200-179390800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr5:179387200-179391200	Strong transcription	HSMMtube	muscle
39	chr5:179387400-179390800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr5:179387400-179395800	Weak transcription	K562	blood
41	chr5:179387800-179390000	Weak transcription	Brain Anterior Caudate	brain
42	chr5:179387800-179391200	Strong transcription	Duodenum Mucosa	Duodenum
43	chr5:179387800-179397000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr5:179387800-179397000	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr5:179388000-179393600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr5:179388000-179394000	Strong transcription	Left Ventricle	heart
47	chr5:179388000-179395000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr5:179388000-179397200	Strong transcription	Adipose Nuclei	Adipose
49	chr5:179388000-179397400	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr5:179388200-179393000	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links