Variant report

Variant	rs28444667
Chromosome Location	chr1:153581823-153581824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:231)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:231 , 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	POLR2A	chr1:153578781-153585928	U87	brain:	n/a	n/a
2	JUN	chr1:153581284-153581959	HUVEC	blood vessel:	n/a	n/a
3	EP300	chr1:153580489-153582132	ECC-1	luminal epithelium:	n/a	chr1:153580785-153580799
4	PBX3	chr1:153581146-153582234	SK-N-SH	brain:	n/a	chr1:153581853-153581862
5	POLR2A	chr1:153580416-153585950	Hela-S3	cervix:	n/a	n/a
6	FOSL2	chr1:153581134-153582064	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr1:153581191-153582124	HepG2	liver:	n/a	n/a
8	TBL1XR1	chr1:153581733-153582231	K562	blood:	n/a	n/a
9	POLR2A	chr1:153580558-153582260	HepG2	liver:	n/a	n/a
10	MAX	chr1:153581311-153582177	K562	blood:	n/a	n/a
11	MYC	chr1:153581252-153582210	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr1:153581108-153582142	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:153578800-153582876	HUVEC	blood vessel:	n/a	n/a
14	JUND	chr1:153581318-153582045	HepG2	liver:	n/a	n/a
15	JUND	chr1:153581287-153582191	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:153580458-153582090	ECC-1	luminal epithelium:	n/a	n/a
17	TBP	chr1:153581728-153582068	K562	blood:	n/a	n/a
18	EP300	chr1:153580431-153582499	MCF-7	breast:	n/a	chr1:153580785-153580799
19	PBX3	chr1:153581205-153582163	A549	lung:	n/a	chr1:153581853-153581862
20	POLR2A	chr1:153581091-153584061	Hela-S3	cervix:	n/a	n/a
21	MYC	chr1:153581788-153582017	HepG2	liver:	n/a	n/a
22	MYC	chr1:153581570-153582262	K562	blood:	n/a	n/a
23	SP1	chr1:153581049-153582298	A549	lung:	n/a	chr1:153581868-153581878 chr1:153581868-153581877 chr1:153581879-153581889 chr1:153581832-153581846
24	TCF12	chr1:153580463-153581888	ECC-1	luminal epithelium:	n/a	chr1:153581050-153581060 chr1:153581524-153581534 chr1:153581015-153581022 chr1:153580817-153580825
25	TAF1	chr1:153581283-153582058	Hela-S3	cervix:	n/a	n/a
26	EGR1	chr1:153580530-153582198	MCF-7	breast:	n/a	chr1:153581357-153581368 chr1:153581351-153581366
27	POLR2A	chr1:153580843-153582539	U87	brain:	n/a	n/a
28	MAX	chr1:153580951-153582503	A549	lung:	n/a	n/a
29	POLR2A	chr1:153581118-153584087	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr1:153581126-153582325	HCT-116	colon:	n/a	n/a
31	TCF12	chr1:153581063-153583011	A549	lung:	n/a	chr1:153581524-153581534
32	TFAP2C	chr1:153580662-153582263	Hela-S3	cervix:	n/a	chr1:153580896-153580911
33	HMGN3	chr1:153581732-153582144	K562	blood:	n/a	n/a
34	MXI1	chr1:153580964-153582308	HepG2	liver:	n/a	n/a
35	GATA3	chr1:153581021-153582062	A549	lung:	n/a	chr1:153581551-153581560
36	HDAC2	chr1:153581658-153582119	HepG2	liver:	n/a	n/a
37	NR2F2	chr1:153580519-153582242	MCF-7	breast:	n/a	n/a
38	MAFK	chr1:153581236-153582034	Hela-S3	cervix:	n/a	n/a
39	FOSL2	chr1:153580567-153582134	MCF-7	breast:	n/a	n/a
40	POLR2A	chr1:153578024-153582691	HUVEC	blood vessel:	n/a	n/a
41	HDAC2	chr1:153580228-153582222	MCF-7	breast:	n/a	chr1:153581238-153581246
42	SMARCC2	chr1:153581117-153583552	Hela-S3	cervix:	n/a	n/a
43	BHLHE40	chr1:153581110-153582092	HepG2	liver:	n/a	chr1:153581428-153581444
44	POLR2A	chr1:153581241-153582106	A549	lung:	n/a	n/a
45	MAX	chr1:153581236-153582061	ECC-1	luminal epithelium:	n/a	n/a
46	NR3C1	chr1:153580963-153582165	A549	lung:	n/a	chr1:153581342-153581368 chr1:153581342-153581368 chr1:153581342-153581368 chr1:153581552-153581561 chr1:153581186-153581200 chr1:153581342-153581368
47	POLR2A	chr1:153581218-153582091	PANC-1	pancreas:	n/a	n/a
48	EP300	chr1:153581752-153582153	K562	blood:	n/a	n/a
49	E2F4	chr1:153581503-153581887	MCF10A-Er-Src	breast:	n/a	n/a
50	MAX	chr1:153581214-153582033	Hela-S3	cervix:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:153581793-153581843	GM12892	blood:	n/a
2	chr1:153581793-153581843	GM12891	blood:	n/a
3	chr1:153581793-153581843	HRPEpiC	eye:	n/a
4	chr1:153581793-153581843	HCPEpiC	choroid plexus:	n/a
5	chr1:153581793-153581843	ECC-1	luminal epithelium:	n/a
6	chr1:153581793-153581843	HRCEpiC	kidney:	n/a
7	chr1:153581793-153581843	SK-N-MC	brain:	n/a
8	chr1:153581793-153581843	HNPCEpiC	eye:	n/a
9	chr1:153581793-153581843	Jurkat	blood:	n/a
10	chr1:153581793-153581843	HCM	heart:	n/a
11	chr1:153581793-153581843	CMK	blood:	n/a
12	chr1:153581793-153581843	GM12878	blood:	n/a
13	chr1:153581793-153581843	ovcar-3	ovarian:	n/a
14	chr1:153581793-153581843	Caco-2	colon:	n/a
15	chr1:153581793-153581843	HCT-116	colon:	n/a
16	chr1:153581793-153581843	HCF	heart:	n/a
17	chr1:153581793-153581843	HEK293	kidney:	embryo
18	chr1:153581793-153581843	SAEC	small airway:	n/a
19	chr1:153581793-153581843	HUVEC	blood vessel:	n/a
20	chr1:153581793-153581843	RPTEC	kidney:	n/a
21	chr1:153581793-153581843	GM19239	blood:	n/a
22	chr1:153581793-153581843	AoSMC	blood vessel:	n/a
23	chr1:153581793-153581843	HAEpiC	amniotic membrane:	n/a
24	chr1:153581793-153581843	MCF-7	breast:	n/a
25	chr1:153581793-153581843	NB4	blood:	n/a
26	chr1:153581793-153581843	LNCaP	prostate:	n/a
27	chr1:153581793-153581843	HMEC	breast:	n/a
28	chr1:153581793-153581843	MCF10A-Er-Src	breast:	n/a
29	chr1:153581793-153581843	BE2_C	brain:	n/a
30	chr1:153581793-153581843	NHBE	bronchial:	n/a
31	chr1:153581793-153581843	HepG2	liver:	n/a
32	chr1:153581793-153581843	H1-hESC	embryonic stem cell:	embryo
33	chr1:153581793-153581843	SKMC	muscle:	n/a
34	chr1:153581793-153581843	SK-N-SH_RA	brain:	n/a
35	chr1:153581793-153581843	Hepatocyte	liver:	n/a
36	chr1:153581793-153581843	HRE	kidney:	n/a
37	chr1:153581793-153581843	A549	lung:	n/a
38	chr1:153581793-153581843	AG09319	gingival:	n/a
39	chr1:153581793-153581843	BJ	skin:	n/a
40	chr1:153581793-153581843	HIPEpiC	eye:	n/a
41	chr1:153581793-153581843	AG04449	skin:	fetal
42	chr1:153581793-153581843	U87	brain:	n/a
43	chr1:153581793-153581843	NH-A	brain:	n/a
44	chr1:153581793-153581843	Hela-S3	cervix:	n/a
45	chr1:153581793-153581843	T-47D	breast:	n/a
46	chr1:153581793-153581843	PANC-1	pancreas:	n/a
47	chr1:153581793-153581843	K562	blood:	n/a
48	chr1:153581793-153581843	AG04450	lung:	fetal
49	chr1:153581793-153581843	AG09309	skin:	n/a
50	chr1:153581793-153581843	GM06990	blood:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153581723..153582287-chr11:62521134..62521681,2	Hela-S3	cervix:
2	chr1:153507285..153510261-chr1:153579792..153582160,3	MCF-7	breast:
3	chr1:153581285..153583404-chr1:153640253..153643290,3	MCF-7	breast:
4	chr1:153581620..153582323-chr17:62223043..62223818,2	Hela-S3	cervix:
5	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
6	chr1:153581196..153582723-chr8:22366793..22368546,2	MCF-7	breast:
7	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
8	chr1:153518244..153520896-chr1:153581745..153584776,3	MCF-7	breast:
9	chr1:153581488..153584174-chr1:153940194..153943077,2	MCF-7	breast:
10	chr1:153580730..153582256-chr1:153699773..153701811,2	MCF-7	breast:
11	chr1:153580088..153583370-chr1:153747776..153750328,4	MCF-7	breast:
12	chr1:153579256..153583611-chr1:153630358..153635573,4	MCF-7	breast:
13	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
14	chr1:153515934..153518266-chr1:153581311..153583180,3	MCF-7	breast:
15	chr1:153519598..153522352-chr1:153580214..153582486,2	K562	blood:
16	chr1:153539321..153541162-chr1:153580987..153583409,2	K562	blood:
17	chr1:153507840..153508475-chr1:153581398..153581986,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
S100A16	TF binding region
S100A16	CpG island
ENSG00000143570	Chromatin interaction
ENSG00000185670	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000120910	Chromatin interaction
ENSG00000188015	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000197956	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11486185	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57058331	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59005288	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61083533	0.93[AFR][1000 genomes]
rs61296485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74115501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118304	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118305	0.93[AFR][1000 genomes]
rs74118306	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118307	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118314	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118316	1.00[AMR][1000 genomes]
rs74118317	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74118318	1.00[AMR][1000 genomes]
rs9700870	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153575000-153582000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:153577800-153582800	Weak transcription	Small Intestine	intestine
3	chr1:153578800-153584800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:153579400-153583600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:153579800-153583000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:153579800-153583600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:153580200-153584800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:153580400-153582000	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr1:153580400-153582200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:153580400-153582800	Transcr. at gene 5' and 3'	NHLF	lung
11	chr1:153580400-153583200	Transcr. at gene 5' and 3'	NHEK	skin
12	chr1:153580600-153582000	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr1:153580600-153582000	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr1:153580600-153582000	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr1:153580600-153582000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
16	chr1:153580600-153582200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:153580600-153582200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:153580600-153582200	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr1:153580600-153582200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr1:153580600-153582400	Enhancers	H1 Cell Line	embryonic stem cell
21	chr1:153580600-153582400	Flanking Active TSS	NH-A	brain
22	chr1:153580600-153583200	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr1:153580600-153583600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:153580800-153582000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:153580800-153582000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
26	chr1:153580800-153582000	Active TSS	HSMMtube	muscle
27	chr1:153580800-153582400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr1:153580800-153582600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:153580800-153582600	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr1:153580800-153582800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:153580800-153582800	Flanking Active TSS	Brain Substantia Nigra	brain
32	chr1:153580800-153583000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr1:153580800-153583200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:153580800-153583200	Flanking Active TSS	Colonic Mucosa	Colon
35	chr1:153580800-153583600	Flanking Active TSS	Osteobl	bone
36	chr1:153581000-153582000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:153581000-153582200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:153581000-153582400	Flanking Active TSS	Hela-S3	cervix
39	chr1:153581000-153583200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:153581000-153583400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr1:153581000-153584000	Enhancers	Colon Smooth Muscle	Colon
42	chr1:153581000-153584200	Enhancers	Fetal Lung	lung
43	chr1:153581200-153582000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:153581200-153582000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:153581200-153582000	Active TSS	HepG2	liver
46	chr1:153581200-153582200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr1:153581200-153582400	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr1:153581200-153582600	Enhancers	H9 Cell Line	embryonic stem cell
49	chr1:153581200-153584200	Enhancers	Gastric	stomach
50	chr1:153581200-153584200	Enhancers	Pancreas	Pancrea

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