Variant report

Variant	rs62052258
Chromosome Location	chr16:81048062-81048063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:81047338..81049033-chr16:81069003..81070847,2	K562	blood:
2	chr16:81041089..81043936-chr16:81047527..81050670,4	MCF-7	breast:
3	chr16:81047016..81048969-chr16:81058785..81061103,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260213	Chromatin interaction
ENSG00000166454	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs62054236	0.82[EUR][1000 genomes]
rs62054247	0.91[EUR][1000 genomes]
rs62054249	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62056081	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948534	chr16:80867635-81160492	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1065258	chr16:80887483-81081768	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv1058045	chr16:80918138-81048242	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1064164	chr16:80918138-81126967	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542991	chr16:80918138-81126967	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv532569	chr16:80980356-81700149	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
7	nsv532597	chr16:81009718-81388348	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
8	nsv573338	chr16:81020393-81106944	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv427984	chr16:81026691-81320341	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62052258	CENPN	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81041800-81053600	Weak transcription	Gastric	stomach
2	chr16:81041800-81069000	Weak transcription	Ovary	ovary
3	chr16:81041800-81069000	Weak transcription	Small Intestine	intestine
4	chr16:81042000-81048200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr16:81042000-81048200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr16:81042000-81053000	Weak transcription	Brain Angular Gyrus	brain
7	chr16:81042000-81053600	Weak transcription	HSMMtube	muscle
8	chr16:81042000-81054400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr16:81042000-81054800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr16:81042000-81057600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr16:81042000-81058400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr16:81042000-81069000	Weak transcription	Esophagus	oesophagus
13	chr16:81042000-81069000	Weak transcription	Pancreas	Pancrea
14	chr16:81042000-81069600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr16:81042200-81048200	Weak transcription	Brain Anterior Caudate	brain
16	chr16:81042200-81052200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr16:81042200-81053600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr16:81042200-81058600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr16:81042200-81068800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr16:81042200-81069000	Weak transcription	Colonic Mucosa	Colon
21	chr16:81042200-81069600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr16:81042400-81049600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr16:81042400-81052400	Weak transcription	Brain Hippocampus Middle	brain
24	chr16:81042400-81056200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr16:81042400-81069000	Weak transcription	Brain Germinal Matrix	brain
26	chr16:81042400-81069000	Weak transcription	Fetal Heart	heart
27	chr16:81042600-81064200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr16:81043000-81059200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr16:81043000-81063800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr16:81043000-81064600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:81043000-81065400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr16:81043200-81062800	Strong transcription	K562	blood
33	chr16:81043200-81065200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr16:81043400-81058800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr16:81044000-81055600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr16:81044000-81057400	Strong transcription	HepG2	liver
37	chr16:81044000-81064400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr16:81044000-81065200	Strong transcription	Thymus	Thymus
39	chr16:81044400-81055800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr16:81044400-81058800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr16:81044400-81059200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr16:81044400-81064000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr16:81044600-81050800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr16:81044600-81058400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr16:81044600-81064000	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr16:81044800-81049000	Strong transcription	Fetal Intestine Large	intestine
47	chr16:81044800-81050600	Strong transcription	NHEK	skin
48	chr16:81044800-81053600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr16:81044800-81058800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr16:81044800-81059000	Strong transcription	Primary monocytes fromperipheralblood	blood

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