Variant report

Variant	rs730688
Chromosome Location	chr5:179704903-179704904
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:179701944..179704923-chr5:179710150..179711887,3	MCF-7	breast:
2	chr5:179698719..179700980-chr5:179701613..179704938,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17627536	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17627815	0.84[CEU][hapmap]
rs17627880	0.80[CEU][hapmap]
rs4441844	0.83[CEU][hapmap]
rs4454029	0.85[CEU][hapmap]
rs55913314	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62404890	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62404891	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6867398	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6882940	0.85[CEU][hapmap];0.91[GIH][hapmap]
rs7708873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7720684	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7722861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs730688	MAPK9	cis	lymphoblastoid	seeQTL
rs730688	RASGEF1C	cis	parietal	SCAN
rs730688	FLT4	cis	cerebellum	SCAN
rs730688	MAPK9	cis	parietal	SCAN
rs730688	MAPK9	cis	cerebellum	SCAN
rs730688	PDLIM7	cis	cerebellum	SCAN
rs730688	MAPK9	Cis_1M	lymphoblastoid	RTeQTL
rs730688	SNCB	cis	parietal	SCAN

Chromatin state (count:124 , 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	chr5:179660800-179706800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:179670200-179712800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:179673600-179705400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:179681800-179705600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:179691200-179706200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:179692800-179705000	Weak transcription	Stomach Mucosa	stomach
9	chr5:179692800-179718000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:179693800-179709600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:179694800-179717600	Weak transcription	HUVEC	blood vessel
12	chr5:179695800-179706200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:179696400-179714800	Weak transcription	Fetal Brain Male	brain
14	chr5:179697600-179710800	Strong transcription	Placenta	Placenta
15	chr5:179698400-179710200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:179698400-179710400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr5:179699000-179705400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:179699000-179705600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:179699000-179707000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:179699000-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:179699200-179707400	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:179699600-179710600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
23	chr5:179699800-179705400	ZNF genes & repeats	Lung	lung
24	chr5:179699800-179707200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr5:179699800-179707600	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr5:179699800-179711400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr5:179699800-179712600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr5:179700000-179706800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:179700000-179711600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
30	chr5:179700200-179710800	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:179700600-179712600	Strong transcription	Primary T cells from cord blood	blood
32	chr5:179700800-179711400	Strong transcription	Fetal Thymus	thymus
33	chr5:179701000-179707200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:179701200-179710800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:179701400-179705400	ZNF genes & repeats	GM12878-XiMat	blood
36	chr5:179701400-179707600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:179701400-179710600	Strong transcription	Fetal Intestine Large	intestine
38	chr5:179701600-179707200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:179701600-179707800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:179701600-179708800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:179701600-179710600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr5:179701800-179710600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr5:179702200-179709600	Strong transcription	Left Ventricle	heart
44	chr5:179702400-179709000	Weak transcription	Fetal Heart	heart
45	chr5:179702400-179709400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:179702400-179714000	Strong transcription	Thymus	Thymus
47	chr5:179702600-179709600	Strong transcription	Fetal Stomach	stomach
48	chr5:179702600-179712200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr5:179702800-179707200	Strong transcription	Adipose Nuclei	Adipose
50	chr5:179702800-179708200	Strong transcription	Rectal Mucosa Donor 31	rectum

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