Variant report

Variant	rs2549889
Chromosome Location	chr16:81071223-81071224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81067084..81072191-chr16:81106033..81112629,21	MCF-7	breast:
2	chr16:81061882..81066764-chr16:81067446..81071538,9	MCF-7	breast:
3	chr16:81067728..81071580-chr16:81109086..81113987,13	K562	blood:
4	chr16:81070898..81072766-chr16:81109747..81111312,2	MCF-7	breast:
5	chr16:81069395..81071569-chr16:81120451..81122846,2	K562	blood:
6	chr16:81068207..81071925-chr16:81073357..81079831,13	MCF-7	breast:
7	chr16:81056423..81058180-chr16:81069392..81072113,2	MCF-7	breast:
8	chr16:81037151..81042784-chr16:81066438..81073797,14	K562	blood:
9	chr16:81037996..81043724-chr16:81066407..81071400,11	MCF-7	breast:
10	chr16:81068173..81071730-chr16:81126382..81131671,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000140905	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000260643	Chromatin interaction
ENSG00000166454	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000261061	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166451	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17763866	1.00[ASN][1000 genomes]
rs2549890	0.84[AFR][1000 genomes]
rs2602432	0.84[AFR][1000 genomes]
rs2602451	0.83[AFR][1000 genomes]
rs2602454	0.83[AFR][1000 genomes]
rs2911157	0.81[AFR][1000 genomes]
rs62054243	1.00[ASN][1000 genomes]
rs62054588	0.81[AMR][1000 genomes]
rs62054592	1.00[ASN][1000 genomes]
rs62054593	1.00[ASN][1000 genomes]
rs62056081	1.00[ASN][1000 genomes]
rs7189182	1.00[ASN][1000 genomes]
rs8058979	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935945	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
4	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
5	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
6	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
7	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
8	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
9	nsv995083	chr16:81050917-81076406	Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv1062724	chr16:81052312-81137007	Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1897	chr16:81060566-81105260	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv2422360	chr16:81066033-81180727	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	esv3374530	chr16:81068676-81071224	Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2549889	CENPN	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81070400-81071400	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr16:81070400-81071400	Enhancers	Spleen	Spleen
3	chr16:81070400-81072600	Weak transcription	Esophagus	oesophagus
4	chr16:81070600-81071400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr16:81070600-81071400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr16:81070600-81071600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:81070600-81072000	Enhancers	Thymus	Thymus
8	chr16:81070600-81072400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr16:81070600-81072600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr16:81070600-81072800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr16:81070600-81073800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:81070600-81075800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr16:81070800-81071400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr16:81070800-81071400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr16:81070800-81071400	Enhancers	Fetal Heart	heart
16	chr16:81070800-81071600	Enhancers	Fetal Brain Male	brain
17	chr16:81070800-81071600	Enhancers	Lung	lung
18	chr16:81070800-81072200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr16:81070800-81072400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr16:81070800-81072400	Enhancers	Colon Smooth Muscle	Colon
21	chr16:81070800-81072400	Genic enhancers	Fetal Stomach	stomach
22	chr16:81070800-81072600	Enhancers	Pancreas	Pancrea
23	chr16:81070800-81073400	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr16:81070800-81073800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr16:81070800-81081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr16:81071000-81071400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr16:81071000-81071400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr16:81071000-81071400	Enhancers	Adipose Nuclei	Adipose
29	chr16:81071000-81071600	Enhancers	Fetal Muscle Leg	muscle
30	chr16:81071000-81071600	Enhancers	Ovary	ovary
31	chr16:81071000-81071800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr16:81071000-81071800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:81071000-81071800	Enhancers	Psoas Muscle	Psoas
34	chr16:81071000-81072200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr16:81071000-81072200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr16:81071000-81072600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr16:81071000-81072800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr16:81071000-81072800	Genic enhancers	Left Ventricle	heart
39	chr16:81071000-81074000	Weak transcription	Primary B cells from cord blood	blood
40	chr16:81071000-81074600	Enhancers	Brain Substantia Nigra	brain
41	chr16:81071000-81074600	Weak transcription	HSMM	muscle
42	chr16:81071000-81075200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr16:81071000-81075200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr16:81071000-81075400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr16:81071000-81075400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr16:81071000-81075800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr16:81071000-81076400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr16:81071000-81079800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr16:81071200-81071400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr16:81071200-81071400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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