Variant report

Variant	rs62406991
Chromosome Location	chr5:179658323-179658324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179656618..179658945-chr5:179717672..179719756,2	MCF-7	breast:
2	chr5:179646868..179648525-chr5:179656321..179659011,2	K562	blood:
3	chr5:179653930..179656240-chr5:179656674..179659051,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000050748	Chromatin interaction
ENSG00000229721	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	0.95[EUR][1000 genomes]
rs17627536	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.85[EUR][1000 genomes]
rs35067749	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35394934	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35551113	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35759987	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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	0.82[EUR][1000 genomes]
rs4700728	0.83[EUR][1000 genomes]
rs4700924	0.85[EUR][1000 genomes]
rs55756747	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406986	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6703	0.88[EUR][1000 genomes]
rs6877489	0.83[EUR][1000 genomes]
rs6882940	0.85[EUR][1000 genomes]
rs6894217	0.98[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
rs62406991	MAPK9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179645600-179660200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:179646800-179659200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:179647600-179659800	Weak transcription	Brain Angular Gyrus	brain
4	chr5:179647600-179660200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:179649600-179660200	Weak transcription	Fetal Brain Female	brain
6	chr5:179650200-179669000	Weak transcription	Fetal Brain Male	brain
7	chr5:179651600-179678000	Weak transcription	Fetal Heart	heart
8	chr5:179652000-179660000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr5:179652400-179660200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:179652800-179659000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr5:179653000-179662800	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:179653200-179660000	Weak transcription	Fetal Lung	lung
13	chr5:179653600-179662400	Weak transcription	Brain Substantia Nigra	brain
14	chr5:179653600-179714600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:179653800-179659400	Weak transcription	Colon Smooth Muscle	Colon
16	chr5:179653800-179662000	Weak transcription	Fetal Thymus	thymus
17	chr5:179654000-179658400	Weak transcription	Left Ventricle	heart
18	chr5:179654000-179659000	Weak transcription	Ovary	ovary
19	chr5:179654000-179660200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:179654000-179661800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:179654200-179659000	Weak transcription	Placenta	Placenta
22	chr5:179654200-179660400	Weak transcription	Fetal Intestine Small	intestine
23	chr5:179654400-179660800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr5:179654800-179660800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:179655000-179679600	Weak transcription	Stomach Mucosa	stomach
26	chr5:179655200-179658400	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:179655200-179663200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr5:179655400-179660600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:179655400-179712600	ZNF genes & repeats	Liver	Liver
30	chr5:179655800-179659400	ZNF genes & repeats	Pancreas	Pancrea
31	chr5:179655800-179661600	ZNF genes & repeats	Lung	lung
32	chr5:179655800-179666400	ZNF genes & repeats	Aorta	Aorta
33	chr5:179655800-179675400	Strong transcription	Primary B cells from cord blood	blood
34	chr5:179656000-179659400	ZNF genes & repeats	Gastric	stomach
35	chr5:179656200-179659200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:179656200-179660200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:179656200-179675000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr5:179656400-179658400	Weak transcription	Primary T cells from cord blood	blood
39	chr5:179656400-179658800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:179656400-179659200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:179656600-179659000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr5:179656600-179660200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:179656600-179703000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
44	chr5:179656800-179659600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr5:179656800-179660200	Weak transcription	Fetal Intestine Large	intestine
46	chr5:179656800-179660800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr5:179656800-179666000	Weak transcription	NH-A	brain
48	chr5:179657000-179658400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr5:179657000-179658400	Weak transcription	Thymus	Thymus
50	chr5:179657000-179660200	Weak transcription	Brain Anterior Caudate	brain

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