Variant report

Variant	rs34428073
Chromosome Location	chr5:179680172-179680173
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	chr5:179680097-179680222	MCF-7	breast:	n/a	n/a
2	POLR2A	chr5:179680157-179680185	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179655112..179657294-chr5:179678114..179680572,2	MCF-7	breast:
2	chr5:179678997..179680660-chr5:179683020..179685571,2	MCF-7	breast:
3	chr5:179679213..179680799-chr5:179687875..179689576,2	K562	blood:

Variant related genes	Relation type
ENSG00000253908	TF binding region
ENSG00000253908	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1127580	0.84[ASN][1000 genomes]
rs11960340	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13162206	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17080136	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17627593	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs33928286	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35203283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56131100	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61478999	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6601104	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6874413	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6875134	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6894217	0.85[ASN][1000 genomes]
rs6895740	0.90[ASN][1000 genomes]
rs6896513	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7710896	0.90[EUR][1000 genomes]
rs7724543	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7730064	0.85[EUR][1000 genomes]
rs7730091	0.85[EUR][1000 genomes]
rs9605	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179653600-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr5:179655400-179712600	ZNF genes & repeats	Liver	Liver
3	chr5:179656600-179703000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
4	chr5:179657800-179697000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:179658800-179680400	Weak transcription	Fetal Kidney	kidney
6	chr5:179660800-179706800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:179665800-179696600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:179666000-179697000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr5:179668200-179696800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
10	chr5:179669400-179683600	Weak transcription	K562	blood
11	chr5:179670200-179681600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:179670200-179712800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:179671200-179694000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
14	chr5:179673600-179691400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:179673600-179694800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr5:179673600-179695200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
17	chr5:179673600-179696600	ZNF genes & repeats	Adipose Nuclei	Adipose
18	chr5:179673600-179697000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:179673600-179697000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
20	chr5:179673600-179701800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
21	chr5:179673600-179705400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:179673800-179696400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:179674200-179680800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:179674200-179680800	ZNF genes & repeats	Aorta	Aorta
25	chr5:179674200-179680800	ZNF genes & repeats	Esophagus	oesophagus
26	chr5:179674200-179680800	ZNF genes & repeats	Gastric	stomach
27	chr5:179674200-179684800	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr5:179674200-179685000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr5:179674200-179685000	ZNF genes & repeats	Colonic Mucosa	Colon
30	chr5:179674200-179685000	ZNF genes & repeats	Lung	lung
31	chr5:179674200-179685000	ZNF genes & repeats	Spleen	Spleen
32	chr5:179674200-179685200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:179674200-179686000	ZNF genes & repeats	Fetal Intestine Large	intestine
34	chr5:179674200-179686200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
35	chr5:179674200-179687000	ZNF genes & repeats	Left Ventricle	heart
36	chr5:179674200-179691400	ZNF genes & repeats	Ovary	ovary
37	chr5:179674200-179691400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
38	chr5:179674200-179696200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:179674200-179696400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:179674200-179696800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
41	chr5:179674400-179682200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:179674400-179692800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
43	chr5:179674400-179694800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:179674600-179694000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
45	chr5:179674800-179681000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:179674800-179684800	ZNF genes & repeats	Fetal Stomach	stomach
47	chr5:179674800-179686600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:179674800-179686800	ZNF genes & repeats	Thymus	Thymus
49	chr5:179674800-179696400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
50	chr5:179675000-179681000	ZNF genes & repeats	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links