Variant report

Variant	rs55756747
Chromosome Location	chr5:179675052-179675053
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179675041..179677707-chr5:179682161..179684985,2	K562	blood:
2	chr5:179666172..179667726-chr5:179673656..179675626,2	MCF-7	breast:
3	chr5:179673735..179676191-chr5:179686105..179688393,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253908	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1127580	0.94[EUR][1000 genomes]
rs17627536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17627815	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17627880	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35067749	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35394934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35551113	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35759987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4270655	0.85[EUR][1000 genomes]
rs4309929	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4441844	0.85[EUR][1000 genomes]
rs4454029	0.85[EUR][1000 genomes]
rs4469167	0.81[EUR][1000 genomes]
rs4700728	0.83[EUR][1000 genomes]
rs4700924	0.85[EUR][1000 genomes]
rs62406986	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62406991	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703	0.87[EUR][1000 genomes]
rs6877489	0.84[EUR][1000 genomes]
rs6882940	0.85[EUR][1000 genomes]
rs6894217	0.99[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55756747	MAPK9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179651600-179678000	Weak transcription	Fetal Heart	heart
2	chr5:179653600-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:179655000-179679600	Weak transcription	Stomach Mucosa	stomach
4	chr5:179655400-179712600	ZNF genes & repeats	Liver	Liver
5	chr5:179655800-179675400	Strong transcription	Primary B cells from cord blood	blood
6	chr5:179656600-179703000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
7	chr5:179657800-179697000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:179658400-179679200	Strong transcription	Primary T cells from cord blood	blood
9	chr5:179658800-179680400	Weak transcription	Fetal Kidney	kidney
10	chr5:179659000-179677600	Strong transcription	Dnd41	blood
11	chr5:179660200-179679800	Weak transcription	HUVEC	blood vessel
12	chr5:179660400-179677600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:179660800-179706800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:179664400-179677000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:179665800-179696600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:179666000-179697000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
17	chr5:179668000-179678400	Weak transcription	Brain Substantia Nigra	brain
18	chr5:179668200-179696800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
19	chr5:179669400-179675200	Weak transcription	Hela-S3	cervix
20	chr5:179669400-179676000	Weak transcription	Psoas Muscle	Psoas
21	chr5:179669400-179683600	Weak transcription	K562	blood
22	chr5:179669800-179678200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
23	chr5:179670200-179681600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:179670200-179712800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:179670400-179676200	Weak transcription	Fetal Brain Male	brain
26	chr5:179671200-179694000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
27	chr5:179672600-179677600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr5:179673000-179675800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:179673000-179677000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:179673200-179675800	Strong transcription	NH-A	brain
31	chr5:179673600-179675200	ZNF genes & repeats	HSMMtube	muscle
32	chr5:179673600-179675800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
33	chr5:179673600-179676000	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr5:179673600-179676200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:179673600-179676200	Strong transcription	Brain Cingulate Gyrus	brain
36	chr5:179673600-179676200	Strong transcription	NHDF-Ad	bronchial
37	chr5:179673600-179676800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:179673600-179677000	Strong transcription	Fetal Lung	lung
39	chr5:179673600-179677200	Strong transcription	Stomach Smooth Muscle	stomach
40	chr5:179673600-179677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:179673600-179677600	Strong transcription	Brain Anterior Caudate	brain
42	chr5:179673600-179677600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
43	chr5:179673600-179677800	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:179673600-179678400	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr5:179673600-179691400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:179673600-179694800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr5:179673600-179695200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
48	chr5:179673600-179696600	ZNF genes & repeats	Adipose Nuclei	Adipose
49	chr5:179673600-179697000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:179673600-179697000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links