Variant report

Variant	rs28528146
Chromosome Location	chr5:126205155-126205156
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:126202154..126203859-chr5:126205061..126207137,2	K562	blood:
2	chr5:126204703..126206861-chr5:126208069..126211338,4	K562	blood:
3	chr5:126203203..126206688-chr5:126207473..126211338,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MARCH3-2	chr5:126203406-126205155	NONHSAT103601

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs4836300	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6864861	0.83[EUR][1000 genomes]
rs6897653	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7449089	0.80[EUR][1000 genomes]
rs7716410	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3330842	chr5:126201653-126205751	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28528146	C5orf63	cis	Nerve Tibial	GTEx
rs28528146	C5orf63	cis	Esophagus Muscularis	GTEx
rs28528146	MARCH3	cis	Muscle Skeletal	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126183600-126210400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:126194400-126208000	Weak transcription	Right Ventricle	heart
3	chr5:126200400-126207800	Weak transcription	Dnd41	blood
4	chr5:126201800-126253400	Weak transcription	A549	lung
5	chr5:126203000-126205200	Enhancers	Spleen	Spleen
6	chr5:126203400-126210800	Weak transcription	Right Atrium	heart
7	chr5:126203600-126210400	Weak transcription	Fetal Heart	heart
8	chr5:126204000-126205400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:126204000-126205400	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr5:126204000-126210800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:126204200-126205200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:126204200-126205400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:126204200-126206400	Weak transcription	K562	blood
14	chr5:126204400-126205200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr5:126204400-126205200	Active TSS	Brain Cingulate Gyrus	brain
16	chr5:126204400-126205200	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr5:126204400-126205200	Enhancers	Placenta	Placenta
18	chr5:126204400-126205400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:126204400-126205400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr5:126204400-126205400	Flanking Active TSS	Fetal Brain Female	brain
21	chr5:126204400-126205600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr5:126204400-126205600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:126204400-126206200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:126204600-126205200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:126204600-126205200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:126204600-126205200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:126204600-126205200	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr5:126204600-126205200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:126204600-126205200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr5:126204600-126205200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr5:126204600-126205200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr5:126204600-126205200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr5:126204600-126205200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:126204600-126205200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr5:126204600-126205200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:126204600-126205200	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr5:126204600-126205200	Active TSS	Brain Hippocampus Middle	brain
38	chr5:126204600-126205200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr5:126204600-126205200	Active TSS	Fetal Kidney	kidney
40	chr5:126204600-126205200	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr5:126204600-126205200	Flanking Active TSS	Fetal Muscle Trunk	muscle
42	chr5:126204600-126205200	Flanking Active TSS	Fetal Thymus	thymus
43	chr5:126204600-126205200	Enhancers	Left Ventricle	heart
44	chr5:126204600-126205200	Genic enhancers	Lung	lung
45	chr5:126204600-126205200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr5:126204600-126205200	Enhancers	Psoas Muscle	Psoas
47	chr5:126204600-126205200	Enhancers	Small Intestine	intestine
48	chr5:126204600-126205200	Flanking Active TSS	Thymus	Thymus
49	chr5:126204600-126205200	Flanking Active TSS	NH-A	brain
50	chr5:126204600-126205400	Active TSS	ES-I3 Cell Line	embryonic stem cell

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