Variant report

Variant	rs2231289
Chromosome Location	chr15:52405498-52405499
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:52405433-52405756	Hela-S3	cervix:	n/a	chr15:52405590-52405601 chr15:52405548-52405559
2	CEBPB	chr15:52405458-52405708	HepG2	liver:	n/a	chr15:52405590-52405601 chr15:52405548-52405559
3	POLR2A	chr15:52403762-52405802	NB4	blood:	n/a	n/a
4	CEBPB	chr15:52405457-52405744	IMR90	lung:	n/a	chr15:52405590-52405601 chr15:52405548-52405559
5	FOS	chr15:52405451-52405679	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr15:52405489-52405629	K562	blood:	n/a	chr15:52405590-52405601 chr15:52405548-52405559
7	MYC	chr15:52404760-52405675	NB4	blood:	n/a	chr15:52405114-52405130 chr15:52405125-52405132 chr15:52405121-52405136
8	EP300	chr15:52405446-52405744	Hela-S3	cervix:	n/a	n/a
9	FOS	chr15:52405479-52405723	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:52405464-52405514	AoSMC	blood vessel:	n/a
2	chr15:52405464-52405514	Jurkat	blood:	n/a
3	chr15:52405464-52405514	NT2-D1	testis:	n/a
4	chr15:52405464-52405514	K562	blood:	n/a
5	chr15:52405464-52405514	LNCaP	prostate:	n/a
6	chr15:52405464-52405514	HAEpiC	amniotic membrane:	n/a
7	chr15:52405464-52405514	AG09309	skin:	n/a
8	chr15:52405464-52405514	ECC-1	luminal epithelium:	n/a
9	chr15:52405464-52405514	HRE	kidney:	n/a
10	chr15:52405464-52405514	NHDF-neo	bronchial:	n/a
11	chr15:52405464-52405514	HIPEpiC	eye:	n/a
12	chr15:52405464-52405514	HNPCEpiC	eye:	n/a
13	chr15:52405464-52405514	AG09319	gingival:	n/a
14	chr15:52405464-52405514	HCT-116	colon:	n/a
15	chr15:52405464-52405514	HEEpiC	esophagus:	n/a
16	chr15:52405464-52405514	HPAEpiC	pulmonary alveolar:	n/a
17	chr15:52405464-52405514	NHBE	bronchial:	n/a
18	chr15:52405464-52405514	HCF	heart:	n/a
19	chr15:52405464-52405514	RPTEC	kidney:	n/a
20	chr15:52405464-52405514	Caco-2	colon:	n/a
21	chr15:52405464-52405514	HRPEpiC	eye:	n/a
22	chr15:52405464-52405514	HepG2	liver:	n/a
23	chr15:52405464-52405514	NB4	blood:	n/a
24	chr15:52405464-52405514	ProgFib	skin:	n/a
25	chr15:52405464-52405514	SKMC	muscle:	n/a
26	chr15:52405464-52405514	U87	brain:	n/a
27	chr15:52405464-52405514	SK-N-MC	brain:	n/a
28	chr15:52405464-52405514	GM12892	blood:	n/a
29	chr15:52405464-52405514	A549	lung:	n/a
30	chr15:52405464-52405514	ovcar-3	ovarian:	n/a
31	chr15:52405464-52405514	Hepatocyte	liver:	n/a
32	chr15:52405464-52405514	HCM	heart:	n/a
33	chr15:52405464-52405514	GM12878	blood:	n/a
34	chr15:52405464-52405514	GM12891	blood:	n/a
35	chr15:52405464-52405514	Hela-S3	cervix:	n/a
36	chr15:52405464-52405514	PFSK-1	brain:	n/a
37	chr15:52405464-52405514	GM19239	blood:	n/a
38	chr15:52405464-52405514	PANC-1	pancreas:	n/a
39	chr15:52405464-52405514	HL-60	blood:	n/a
40	chr15:52405464-52405514	HUVEC	blood vessel:	n/a
41	chr15:52405464-52405514	HRCEpiC	kidney:	n/a
42	chr15:52405464-52405514	BJ	skin:	n/a
43	chr15:52405464-52405514	AG04449	skin:	fetal
44	chr15:52405464-52405514	MCF10A-Er-Src	breast:	n/a
45	chr15:52405464-52405514	GM06990	blood:	n/a
46	chr15:52405464-52405514	NH-A	brain:	n/a
47	chr15:52405464-52405514	HEK293	kidney:	embryo
48	chr15:52405464-52405514	AG10803	skin:	n/a
49	chr15:52405464-52405514	T-47D	breast:	n/a
50	chr15:52405464-52405514	AG04450	lung:	fetal

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52263208..52265625-chr15:52404085..52407650,4	MCF-7	breast:
2	chr15:52404951..52408390-chr15:52415652..52417848,3	K562	blood:
3	chr15:52404587..52406331-chr15:52432467..52434245,2	MCF-7	breast:
4	chr15:52403961..52406655-chr15:52470750..52472609,2	MCF-7	breast:
5	chr15:52404464..52407280-chr15:52415315..52418015,2	MCF-7	breast:
6	chr15:52309956..52312123-chr15:52404856..52406463,2	MCF-7	breast:

No data

Variant related genes	Relation type
BCL2L10	TF binding region
ENSG00000259327	TF binding region
BCL2L10	CpG island
ENSG00000259327	CpG island
ENSG00000166477	Chromatin interaction
ENSG00000259709	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000259438	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16964751	1.00[AMR][1000 genomes]
rs16964760	1.00[AMR][1000 genomes]
rs16964764	1.00[AMR][1000 genomes]
rs17540171	1.00[AFR][1000 genomes]
rs17540546	0.94[AMR][1000 genomes]
rs17540734	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs17612637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17612796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35581121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41277704	0.94[AMR][1000 genomes]
rs41277706	0.94[AMR][1000 genomes]
rs41277712	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4776006	1.00[AMR][1000 genomes]
rs4776018	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4776019	0.94[AMR][1000 genomes]
rs62016465	1.00[AMR][1000 genomes]
rs62016466	1.00[AMR][1000 genomes]
rs7168334	1.00[AMR][1000 genomes]
rs7181736	1.00[AMR][1000 genomes]
rs74015635	0.83[AMR][1000 genomes]
rs8024846	0.94[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52402200-52411400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:52402400-52405600	Weak transcription	HepG2	liver
3	chr15:52404800-52405600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr15:52404800-52405800	Active TSS	Duodenum Mucosa	Duodenum
5	chr15:52404800-52405800	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr15:52404800-52406600	Weak transcription	Brain Anterior Caudate	brain
7	chr15:52404800-52406800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:52404800-52407600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:52404800-52407800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:52404800-52408000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr15:52404800-52408200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:52404800-52408400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr15:52404800-52409800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:52404800-52410600	Enhancers	Adipose Nuclei	Adipose
15	chr15:52404800-52416400	Weak transcription	Aorta	Aorta
16	chr15:52404800-52428000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr15:52405000-52405600	Weak transcription	GM12878-XiMat	blood
18	chr15:52405000-52405800	Bivalent Enhancer	Fetal Intestine Large	intestine
19	chr15:52405000-52406200	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:52405000-52406200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr15:52405000-52406400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:52405000-52406400	Weak transcription	Pancreas	Pancrea
23	chr15:52405000-52406600	Weak transcription	Brain Angular Gyrus	brain
24	chr15:52405000-52406600	Weak transcription	Brain Substantia Nigra	brain
25	chr15:52405000-52407600	Weak transcription	HUVEC	blood vessel
26	chr15:52405000-52407800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr15:52405000-52407800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:52405000-52408000	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:52405000-52408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:52405000-52408400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr15:52405000-52409800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:52405000-52411800	Weak transcription	Ovary	ovary
33	chr15:52405000-52412000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:52405000-52413200	Weak transcription	Primary T cells from cord blood	blood
35	chr15:52405000-52414800	Weak transcription	Primary B cells from cord blood	blood
36	chr15:52405000-52416400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr15:52405000-52416400	Weak transcription	Gastric	stomach
38	chr15:52405000-52416600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr15:52405000-52416600	Weak transcription	Esophagus	oesophagus
40	chr15:52405000-52420400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr15:52405000-52421800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr15:52405000-52427400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:52405000-52427800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:52405000-52428800	Weak transcription	Fetal Heart	heart
45	chr15:52405200-52406200	Weak transcription	Fetal Brain Male	brain
46	chr15:52405200-52406400	Enhancers	Fetal Intestine Small	intestine
47	chr15:52405200-52406800	Weak transcription	Liver	Liver
48	chr15:52405200-52407600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:52405200-52407800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:52405200-52408200	Weak transcription	Primary T helper cells PMA-I stimulated	--

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