Variant report

Variant	rs1669854
Chromosome Location	chr15:45004324-45004325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:233)
CpG islands
(count:61)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:233 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr15:45003248-45004328	HepG2	liver:	n/a	n/a
2	MXI1	chr15:45003069-45005114	K562	blood:	n/a	n/a
3	MAX	chr15:45003327-45005151	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:45002354-45013577	GM18951	blood:	n/a	n/a
5	MAX	chr15:45003207-45005188	SK-N-SH	brain:	n/a	n/a
6	RCOR1	chr15:45002787-45004443	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr15:45002647-45005444	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr15:45002280-45010248	GM12891	blood:	n/a	n/a
9	GATA2	chr15:45002956-45004428	SH-SY5Y	brain:	n/a	n/a
10	POLR2A	chr15:45002339-45005459	K562	blood:	n/a	n/a
11	POLR2A	chr15:45002253-45014109	GM12892	blood:	n/a	n/a
12	WRNIP1	chr15:45002331-45005445	GM12878	blood:	n/a	n/a
13	POU2F2	chr15:45003264-45004509	GM12878	blood:	n/a	chr15:45004172-45004184
14	ETS1	chr15:45003422-45004597	GM12878	blood:	n/a	chr15:45004250-45004261
15	E2F6	chr15:45003579-45004675	A549	lung:	n/a	chr15:45004142-45004150 chr15:45003664-45003673 chr15:45004202-45004209 chr15:45004142-45004150
16	BCLAF1	chr15:45002272-45005506	GM12878	blood:	n/a	chr15:45003027-45003040 chr15:45003589-45003598 chr15:45003959-45003972 chr15:45003029-45003038 chr15:45005259-45005267 chr15:45003577-45003586 chr15:45004128-45004137
17	EP300	chr15:45004285-45004958	GM12878	blood:	n/a	n/a
18	FOXM1	chr15:45002235-45005519	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:45002358-45005169	K562	blood:	n/a	n/a
20	POLR2A	chr15:45002760-45005424	Hela-S3	cervix:	n/a	n/a
21	STAT5A	chr15:45002250-45005134	GM12878	blood:	n/a	chr15:45003985-45003997 chr15:45003025-45003037 chr15:45003571-45003582 chr15:45004126-45004137 chr15:45002510-45002522 chr15:45003315-45003326 chr15:45004890-45004901 chr15:45003086-45003094 chr15:45003840-45003852
22	CREB1	chr15:45003243-45004333	K562	blood:	n/a	n/a
23	POLR2A	chr15:45002255-45010226	GM12891	blood:	n/a	n/a
24	MYC	chr15:45002400-45005143	K562	blood:	n/a	n/a
25	POLR2A	chr15:45003220-45005427	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:45003277-45004434	K562	blood:	n/a	n/a
27	CBX3	chr15:45003119-45004589	K562	blood:	n/a	n/a
28	UBTF	chr15:45003209-45005150	K562	blood:	n/a	n/a
29	TBL1XR1	chr15:45002321-45008799	GM12878	blood:	n/a	n/a
30	GATA1	chr15:45002260-45005291	PBDE	blood:	n/a	chr15:45002520-45002529
31	MYBL2	chr15:45003104-45004469	HepG2	liver:	n/a	n/a
32	ELF1	chr15:45003919-45004347	K562	blood:	n/a	chr15:45004130-45004143
33	POLR2A	chr15:45002339-45005048	NB4	blood:	n/a	n/a
34	MAX	chr15:45003163-45005246	K562	blood:	n/a	n/a
35	KAT2A	chr15:45003408-45004760	GM12878	blood:	n/a	n/a
36	CREB1	chr15:45003203-45004416	HepG2	liver:	n/a	n/a
37	POLR2A	chr15:45002045-45013680	GM18505	blood:	n/a	n/a
38	POLR2A	chr15:45003153-45005141	U87	brain:	n/a	n/a
39	NR2F2	chr15:45003175-45005294	K562	blood:	n/a	n/a
40	POLR2A	chr15:45004066-45004465	HCT-116	colon:	n/a	n/a
41	MAX	chr15:45004206-45004763	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr15:45002139-45014682	GM12878	blood:	n/a	n/a
43	NFIC	chr15:45004140-45005004	GM12878	blood:	n/a	n/a
44	MYC	chr15:45004316-45004326	K562	blood:	n/a	n/a
45	CUX1	chr15:45004291-45004563	K562	blood:	n/a	n/a
46	BHLHE40	chr15:45002454-45005066	K562	blood:	n/a	n/a
47	POLR2A	chr15:45003113-45004405	HepG2	liver:	n/a	n/a
48	POLR2A	chr15:45002460-45004424	K562	blood:	n/a	n/a
49	BHLHE40	chr15:45002348-45005461	GM12878	blood:	n/a	n/a
50	RCOR1	chr15:45002143-45005160	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:45004323-45004373	HepG2	liver:	n/a
2	chr15:45004323-45004373	SAEC	small airway:	n/a
3	chr15:45004323-45004373	HCM	heart:	n/a
4	chr15:45004323-45004373	H1-hESC	embryonic stem cell:	embryo
5	chr15:45004323-45004373	AoSMC	blood vessel:	n/a
6	chr15:45004323-45004373	HRPEpiC	eye:	n/a
7	chr15:45004323-45004373	RPTEC	kidney:	n/a
8	chr15:45004323-45004373	SK-N-SH	brain:	n/a
9	chr15:45004323-45004373	LNCaP	prostate:	n/a
10	chr15:45004323-45004373	HMEC	breast:	n/a
11	chr15:45004323-45004373	PFSK-1	brain:	n/a
12	chr15:45004323-45004373	U87	brain:	n/a
13	chr15:45004323-45004373	HNPCEpiC	eye:	n/a
14	chr15:45004323-45004373	GM19239	blood:	n/a
15	chr15:45004323-45004373	NHBE	bronchial:	n/a
16	chr15:45004323-45004373	MCF10A-Er-Src	breast:	n/a
17	chr15:45004323-45004373	ProgFib	skin:	n/a
18	chr15:45004323-45004373	PrEC	prostate:	n/a
19	chr15:45004323-45004373	Hela-S3	cervix:	n/a
20	chr15:45004323-45004373	HEK293	kidney:	embryo
21	chr15:45004323-45004373	AG09309	skin:	n/a
22	chr15:45004323-45004373	GM12892	blood:	n/a
23	chr15:45004323-45004373	NT2-D1	testis:	n/a
24	chr15:45004323-45004373	HCT-116	colon:	n/a
25	chr15:45004323-45004373	T-47D	breast:	n/a
26	chr15:45004323-45004373	SK-N-MC	brain:	n/a
27	chr15:45004323-45004373	HIPEpiC	eye:	n/a
28	chr15:45004323-45004373	IMR90	lung:	fetal
29	chr15:45004323-45004373	ovcar-3	ovarian:	n/a
30	chr15:45004323-45004373	AG10803	skin:	n/a
31	chr15:45004323-45004373	Caco-2	colon:	n/a
32	chr15:45004323-45004373	K562	blood:	n/a
33	chr15:45004323-45004373	BJ	skin:	n/a
34	chr15:45004323-45004373	NH-A	brain:	n/a
35	chr15:45004323-45004373	BE2_C	brain:	n/a
36	chr15:45004323-45004373	HPAEpiC	pulmonary alveolar:	n/a
37	chr15:45004323-45004373	HCF	heart:	n/a
38	chr15:45004323-45004373	Hepatocyte	liver:	n/a
39	chr15:45004323-45004373	HUVEC	blood vessel:	n/a
40	chr15:45004323-45004373	HCPEpiC	choroid plexus:	n/a
41	chr15:45004323-45004373	AG04449	skin:	fetal
42	chr15:45004323-45004373	SK-N-SH_RA	brain:	n/a
43	chr15:45004323-45004373	A549	lung:	n/a
44	chr15:45004323-45004373	AG04450	lung:	fetal
45	chr15:45004323-45004373	CMK	blood:	n/a
46	chr15:45004323-45004373	Jurkat	blood:	n/a
47	chr15:45004323-45004373	HRCEpiC	kidney:	n/a
48	chr15:45004323-45004373	HAEpiC	amniotic membrane:	n/a
49	chr15:45004323-45004373	SKMC	muscle:	n/a
50	chr15:45004323-45004373	NB4	blood:	n/a

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49524746..49525589-chr15:45003629..45004506,2	Hela-S3	cervix:
2	chr15:44966253..44968206-chr15:45002502..45005118,3	MCF-7	breast:
3	chr15:45003614..45004535-chr3:32611979..32612834,2	Hela-S3	cervix:
4	chr15:44958042..44960348-chr15:45002239..45005135,4	K562	blood:
5	chr15:44951739..44957508-chr15:45000588..45008057,33	K562	blood:
6	chr15:44980888..44990623-chr15:45002366..45006726,14	K562	blood:
7	chr15:44952988..44962373-chr15:45002018..45007307,26	MCF-7	breast:
8	chr15:44888819..44891179-chr15:45002338..45004716,3	K562	blood:
9	chr15:45003756..45004547-chr19:1478772..1479552,2	Hela-S3	cervix:
10	chr12:49110072..49110682-chr15:45004204..45004868,2	Hela-S3	cervix:
11	chr12:121975261..121976230-chr15:45004204..45004901,2	Hela-S3	cervix:
12	chr1:23670320..23671266-chr15:45003710..45004619,2	Hela-S3	cervix:
13	chr15:44968315..44970113-chr15:45003699..45005679,2	MCF-7	breast:
14	chr15:44968819..44972092-chr15:45002551..45007992,5	K562	blood:
15	chr12:54674280..54674997-chr15:45003778..45004683,2	Hela-S3	cervix:
16	chr15:45000863..45005844-chr15:45018710..45023352,9	MCF-7	breast:
17	chr15:44951575..44958275-chr15:45001046..45006983,19	MCF-7	breast:
18	chr15:44952188..44965604-chr15:45001074..45012963,51	K562	blood:

No data

Variant related genes	Relation type
PATL2	TF binding region
B2M	TF binding region
PATL2	CpG island
B2M	CpG island
ENSG00000125944	Chromatin interaction
ENSG00000206957	Chromatin interaction
ENSG00000185880	Chromatin interaction
ENSG00000229474	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000144635	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000119559	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1288094	1.00[AMR][1000 genomes]
rs1901536	0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1901539	1.00[AMR][1000 genomes]
rs2167594	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2254602	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2444005	1.00[YRI][hapmap]
rs2444007	0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2444011	1.00[AMR][1000 genomes]
rs2462044	1.00[AMR][1000 genomes]
rs2468072	1.00[AMR][1000 genomes]
rs2470916	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs2960207	1.00[AMR][1000 genomes]
rs3100129	1.00[AMR][1000 genomes]
rs3100130	1.00[AMR][1000 genomes]
rs3100144	1.00[AMR][1000 genomes]
rs3100145	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3110178	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3110179	0.84[AFR][1000 genomes]
rs3110180	1.00[AMR][1000 genomes]
rs3110673	1.00[AMR][1000 genomes]
rs3110674	1.00[AMR][1000 genomes]
rs34359070	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34387827	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34708122	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4625702	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4923992	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4923994	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6493125	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	135 gene(s)	inside rSNPs	diseases
2	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
4	nsv832990	chr15:44990765-45162714	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 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	chr15:45001400-45005200	Active TSS	GM12878-XiMat	blood
2	chr15:45002000-45005600	Active TSS	Colon Smooth Muscle	Colon
3	chr15:45002000-45005800	Active TSS	Brain Anterior Caudate	brain
4	chr15:45002000-45006000	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr15:45002200-45005800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr15:45002200-45006800	Active TSS	Colonic Mucosa	Colon
7	chr15:45002400-45004400	Active TSS	Primary B cells from cord blood	blood
8	chr15:45002400-45005000	Active TSS	Adipose Nuclei	Adipose
9	chr15:45002400-45005400	Active TSS	Brain Cingulate Gyrus	brain
10	chr15:45002400-45005400	Active TSS	Spleen	Spleen
11	chr15:45002400-45005600	Active TSS	Rectal Smooth Muscle	rectum
12	chr15:45002400-45005600	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr15:45002400-45006000	Active TSS	NHLF	lung
14	chr15:45002400-45006400	Active TSS	Sigmoid Colon	Sigmoid Colon
15	chr15:45002400-45006600	Active TSS	Lung	lung
16	chr15:45002400-45006600	Active TSS	Stomach Smooth Muscle	stomach
17	chr15:45002400-45006800	Active TSS	Small Intestine	intestine
18	chr15:45002400-45007000	Active TSS	Left Ventricle	heart
19	chr15:45002400-45007200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr15:45002400-45007200	Active TSS	Right Ventricle	heart
21	chr15:45002600-45004400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:45002600-45004800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:45002600-45004800	Active TSS	Fetal Muscle Trunk	muscle
24	chr15:45002600-45005200	Active TSS	Muscle Satellite Cultured Cells	--
25	chr15:45002600-45005200	Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr15:45002600-45005200	Active TSS	Osteobl	bone
27	chr15:45002600-45005400	Active TSS	HSMM	muscle
28	chr15:45002600-45005600	Active TSS	NHEK	skin
29	chr15:45002600-45005800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:45002600-45005800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:45002600-45005800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr15:45002600-45006200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:45002600-45006200	Active TSS	Duodenum Mucosa	Duodenum
34	chr15:45002600-45006400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:45002600-45007200	Active TSS	Psoas Muscle	Psoas
36	chr15:45002800-45004400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:45002800-45004400	Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr15:45002800-45004400	Active TSS	Primary T cells fromperipheralblood	blood
39	chr15:45002800-45004400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:45002800-45004600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:45002800-45004600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr15:45002800-45004800	Active TSS	Fetal Lung	lung
43	chr15:45002800-45004800	Active TSS	Fetal Muscle Leg	muscle
44	chr15:45002800-45005000	Active TSS	H9 Cell Line	embryonic stem cell
45	chr15:45002800-45005000	Active TSS	Fetal Intestine Large	intestine
46	chr15:45002800-45005000	Active TSS	Fetal Intestine Small	intestine
47	chr15:45002800-45005000	Active TSS	Placenta Amnion	Placenta Amnion
48	chr15:45002800-45005200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:45002800-45005200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:45002800-45005200	Active TSS	HMEC	breast

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