Variant report

Variant	rs2549876
Chromosome Location	chr16:81039234-81039235
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:61)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr16:81039180-81039330	HEEpiC	esophagus:	n/a	n/a
2	HEY1	chr16:81039121-81039612	K562	blood:	n/a	n/a
3	TEAD4	chr16:81039232-81039678	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr16:81039155-81041501	A549	lung:	n/a	chr16:81040795-81040805 chr16:81040695-81040704 chr16:81041155-81041164
5	POLR2A	chr16:81039052-81041720	H1-hESC	embryonic stem cell:	n/a	n/a
6	WRNIP1	chr16:81039162-81039575	GM12878	blood:	n/a	n/a
7	IRF1	chr16:81039214-81041494	K562	blood:	n/a	chr16:81039570-81039584 chr16:81039573-81039587 chr16:81041214-81041225 chr16:81041214-81041226 chr16:81039575-81039591 chr16:81039572-81039585 chr16:81041214-81041226 chr16:81039572-81039586 chr16:81040780-81040794
8	MAX	chr16:81039205-81039664	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr16:81039134-81041558	Hela-S3	cervix:	n/a	n/a
10	JUN	chr16:81039044-81041495	K562	blood:	n/a	chr16:81041079-81041088 chr16:81041078-81041091
11	MXI1	chr16:81039145-81042276	SK-N-SH	brain:	n/a	n/a
12	SMARCC1	chr16:81039221-81041876	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr16:81038829-81041850	Hela-S3	cervix:	n/a	n/a
14	HCFC1	chr16:81039075-81042051	Hela-S3	cervix:	n/a	n/a
15	ZBTB7A	chr16:81039091-81039376	K562	blood:	n/a	n/a
16	TEAD4	chr16:81039194-81040285	HepG2	liver:	n/a	n/a
17	MAX	chr16:81039205-81039688	K562	blood:	n/a	n/a
18	CHD1	chr16:81039191-81042059	IMR90	lung:	n/a	chr16:81041086-81041096
19	EBF1	chr16:81039212-81039266	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr16:81039227-81039277	Hepatocyte	liver:	n/a
2	chr16:81039227-81039277	AG09309	skin:	n/a
3	chr16:81039227-81039277	BE2_C	brain:	n/a
4	chr16:81039227-81039277	AG04449	skin:	fetal
5	chr16:81039227-81039277	HEK293	kidney:	embryo
6	chr16:81039227-81039277	HIPEpiC	eye:	n/a
7	chr16:81039227-81039277	LNCaP	prostate:	n/a
8	chr16:81039227-81039277	SKMC	muscle:	n/a
9	chr16:81039227-81039277	GM19239	blood:	n/a
10	chr16:81039227-81039277	T-47D	breast:	n/a
11	chr16:81039227-81039277	HUVEC	blood vessel:	n/a
12	chr16:81039227-81039277	NB4	blood:	n/a
13	chr16:81039227-81039277	PrEC	prostate:	n/a
14	chr16:81039227-81039277	HCPEpiC	choroid plexus:	n/a
15	chr16:81039227-81039277	IMR90	lung:	fetal
16	chr16:81039227-81039277	MCF10A-Er-Src	breast:	n/a
17	chr16:81039227-81039277	ovcar-3	ovarian:	n/a
18	chr16:81039227-81039277	GM06990	blood:	n/a
19	chr16:81039227-81039277	HCF	heart:	n/a
20	chr16:81039227-81039277	SK-N-MC	brain:	n/a
21	chr16:81039227-81039277	HPAEpiC	pulmonary alveolar:	n/a
22	chr16:81039227-81039277	Jurkat	blood:	n/a
23	chr16:81039227-81039277	HRCEpiC	kidney:	n/a
24	chr16:81039227-81039277	PFSK-1	brain:	n/a
25	chr16:81039227-81039277	MCF-7	breast:	n/a
26	chr16:81039227-81039277	AG04450	lung:	fetal
27	chr16:81039227-81039277	NHBE	bronchial:	n/a
28	chr16:81039227-81039277	HNPCEpiC	eye:	n/a
29	chr16:81039227-81039277	A549	lung:	n/a
30	chr16:81039227-81039277	GM12892	blood:	n/a
31	chr16:81039227-81039277	AoSMC	blood vessel:	n/a
32	chr16:81039227-81039277	ECC-1	luminal epithelium:	n/a
33	chr16:81039227-81039277	SAEC	small airway:	n/a
34	chr16:81039227-81039277	HCM	heart:	n/a
35	chr16:81039227-81039277	ProgFib	skin:	n/a
36	chr16:81039227-81039277	K562	blood:	n/a
37	chr16:81039227-81039277	HEEpiC	esophagus:	n/a
38	chr16:81039227-81039277	HL-60	blood:	n/a
39	chr16:81039227-81039277	HRPEpiC	eye:	n/a
40	chr16:81039227-81039277	AG10803	skin:	n/a
41	chr16:81039227-81039277	HAEpiC	amniotic membrane:	n/a
42	chr16:81039227-81039277	Caco-2	colon:	n/a
43	chr16:81039227-81039277	Hela-S3	cervix:	n/a
44	chr16:81039227-81039277	HCT-116	colon:	n/a
45	chr16:81039227-81039277	GM12878	blood:	n/a
46	chr16:81039227-81039277	H1-hESC	embryonic stem cell:	embryo
47	chr16:81039227-81039277	NHDF-neo	bronchial:	n/a
48	chr16:81039227-81039277	SK-N-SH	brain:	n/a
49	chr16:81039227-81039277	HRE	kidney:	n/a
50	chr16:81039227-81039277	HMEC	breast:	n/a

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:81025473..81027772-chr16:81037035..81041311,4	K562	blood:
2	chr16:81038258..81040784-chr16:81347032..81349945,2	K562	blood:
3	chr16:81038105..81044923-chr16:81066300..81070952,14	MCF-7	breast:
4	chr16:81037151..81044642-chr16:81065528..81070966,16	K562	blood:
5	chr16:81028135..81034571-chr16:81035246..81044200,13	K562	blood:
6	chr16:81038653..81041025-chr16:81346635..81349129,2	MCF-7	breast:
7	chr16:81037996..81043724-chr16:81066407..81071400,11	MCF-7	breast:
8	chr16:81038376..81042418-chr16:81108432..81111584,4	K562	blood:
9	chr16:81037094..81043910-chr16:81050858..81058489,11	MCF-7	breast:
10	chr16:81039002..81041272-chr16:81057250..81059847,2	MCF-7	breast:
11	chr16:81000562..81002901-chr16:81037638..81039411,2	K562	blood:
12	chr16:81038376..81043277-chr16:81108432..81112403,6	K562	blood:
13	chr16:81038922..81040878-chr16:81128552..81130305,2	MCF-7	breast:
14	chr16:81037151..81042784-chr16:81066438..81073797,14	K562	blood:
15	chr16:81036155..81041262-chr16:81074086..81079875,7	K562	blood:

No data

Variant related genes	Relation type
CENPN	TF binding region
CENPN	CpG island
ENSG00000261609	Chromatin interaction
ENSG00000103121	Chromatin interaction
ENSG00000260213	Chromatin interaction
ENSG00000260495	Chromatin interaction
ENSG00000166455	Chromatin interaction
ENSG00000245059	Chromatin interaction
ENSG00000166454	Chromatin interaction
ENSG00000166451	Chromatin interaction
ENSG00000140905	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1349755	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2167887	0.81[AFR][1000 genomes]
rs2194320	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2549878	0.92[AFR][1000 genomes]
rs2549880	0.89[AFR][1000 genomes]
rs2549881	0.86[AFR][1000 genomes]
rs2602420	1.00[AMR][1000 genomes]
rs2602421	1.00[AMR][1000 genomes]
rs28430837	1.00[AMR][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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81035600-81039400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr16:81036000-81039400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr16:81036600-81039400	Enhancers	Fetal Heart	heart
4	chr16:81036600-81039400	Enhancers	Fetal Lung	lung
5	chr16:81036600-81039400	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr16:81037200-81039600	Flanking Active TSS	Dnd41	blood
7	chr16:81037600-81039600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr16:81037600-81039600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr16:81037600-81039600	Flanking Active TSS	Stomach Smooth Muscle	stomach
10	chr16:81037600-81039800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr16:81037600-81039800	Enhancers	Small Intestine	intestine
12	chr16:81037600-81040000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr16:81037800-81039600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr16:81037800-81039600	Flanking Active TSS	HUVEC	blood vessel
15	chr16:81037800-81040000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr16:81037800-81040000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr16:81037800-81042000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr16:81037800-81042400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr16:81038000-81039400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:81038000-81039800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr16:81038000-81040000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr16:81038200-81039400	Enhancers	Primary B cells from peripheral blood	blood
23	chr16:81038200-81041800	Active TSS	Ovary	ovary
24	chr16:81038200-81041800	Active TSS	Hela-S3	cervix
25	chr16:81038200-81042000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr16:81038200-81042400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr16:81038400-81039400	Enhancers	Primary T cells from cord blood	blood
28	chr16:81038400-81042000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr16:81038400-81042200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr16:81038400-81042200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr16:81038600-81039400	Enhancers	Pancreas	Pancrea
32	chr16:81038600-81039400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr16:81038600-81039400	Bivalent/Poised TSS	HepG2	liver
34	chr16:81038600-81039600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr16:81038600-81039800	Flanking Active TSS	NH-A	brain
36	chr16:81038600-81040000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr16:81038800-81039400	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr16:81038800-81039600	Flanking Active TSS	Placenta	Placenta
39	chr16:81038800-81039800	Enhancers	Spleen	Spleen
40	chr16:81038800-81041800	Active TSS	Left Ventricle	heart
41	chr16:81038800-81042000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr16:81038800-81042200	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr16:81038800-81042200	Active TSS	A549	lung
44	chr16:81038800-81042400	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr16:81039000-81039600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr16:81039000-81039600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr16:81039000-81039600	Flanking Active TSS	HMEC	breast
48	chr16:81039000-81039600	Flanking Active TSS	HSMM	muscle
49	chr16:81039000-81039600	Flanking Active TSS	NHDF-Ad	bronchial
50	chr16:81039000-81039800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

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