Variant report

Variant	rs28406419
Chromosome Location	chr5:102883021-102883022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:102882600..102886619-chr5:102891245..102894545,3	K562	blood:
2	chr5:102875511..102879906-chr5:102880886..102883676,4	K562	blood:
3	chr5:102881714..102883723-chr5:102890100..102892404,3	K562	blood:

Variant related genes	Relation type
ENSG00000248757	Chromatin interaction
ENSG00000112874	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10057864	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061242	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10078744	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737902	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750858	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13157247	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356231	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34672333	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35355522	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797900	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878912	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880267	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71586376	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73190066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707836	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716935	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7723689	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725090	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730302	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734923	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327885	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv882523	chr5:102687151-103342745	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1031600	chr5:102728430-103013575	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1025561	chr5:102744280-103152495	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv537832	chr5:102744280-103152495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1025859	chr5:102744479-103710290	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv537833	chr5:102744479-103710290	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28406419	NUDT12	cis	Adipose Subcutaneous	GTEx
rs28406419	NUDT12	Cis_1M	lymphoblastoid	RTeQTL
rs28406419	NUDT12	cis	Skin Sun Exposed Lower leg	GTEx
rs28406419	NUDT12	cis	Esophagus Mucosa	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:102874200-102897400	Weak transcription	Pancreas	Pancrea
2	chr5:102875400-102887800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:102875800-102897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:102876600-102886000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:102876800-102887800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:102877000-102886000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:102877200-102888000	Weak transcription	Stomach Mucosa	stomach
8	chr5:102878400-102887800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:102878600-102885800	Weak transcription	Osteobl	bone
10	chr5:102878800-102886400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:102879800-102897200	Weak transcription	Brain Germinal Matrix	brain
12	chr5:102879800-102897400	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:102880000-102885400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:102880200-102886600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:102880200-102886800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:102880200-102897200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:102880800-102886600	Weak transcription	Left Ventricle	heart
18	chr5:102881000-102885400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:102881200-102884800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:102881200-102897800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:102882200-102883200	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr5:102882200-102886800	Weak transcription	HSMM	muscle
23	chr5:102882400-102883200	Enhancers	GM12878-XiMat	blood
24	chr5:102882400-102897400	Weak transcription	Psoas Muscle	Psoas
25	chr5:102882800-102897400	Weak transcription	Fetal Heart	heart
26	chr5:102882800-102897600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:102883000-102889200	Weak transcription	Colon Smooth Muscle	Colon

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