Variant report

Variant	rs61296485
Chromosome Location	chr1:153581415-153581416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	JUN	chr1:153581338-153581687	HepG2	liver:	n/a	n/a
4	EP300	chr1:153580489-153582132	ECC-1	luminal epithelium:	n/a	chr1:153580785-153580799
5	STAT3	chr1:153581323-153581681	Hela-S3	cervix:	n/a	n/a
6	PBX3	chr1:153581146-153582234	SK-N-SH	brain:	n/a	chr1:153581853-153581862
7	POLR2A	chr1:153581376-153581460	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:153580416-153585950	Hela-S3	cervix:	n/a	n/a
9	FOS	chr1:153581263-153581747	MCF10A-Er-Src	breast:	n/a	chr1:153581551-153581562
10	POLR2A	chr1:153581342-153581516	A549	lung:	n/a	n/a
11	FOSL2	chr1:153581134-153582064	SK-N-SH	brain:	n/a	n/a
12	FOXA2	chr1:153581173-153581552	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:153581191-153582124	HepG2	liver:	n/a	n/a
14	POLR2A	chr1:153580558-153582260	HepG2	liver:	n/a	n/a
15	MAX	chr1:153581311-153582177	K562	blood:	n/a	n/a
16	STAT3	chr1:153581276-153581687	MCF10A-Er-Src	breast:	n/a	n/a
17	STAT3	chr1:153581335-153581553	MCF10A-Er-Src	breast:	n/a	n/a
18	MYC	chr1:153581252-153582210	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr1:153581108-153582142	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:153578800-153582876	HUVEC	blood vessel:	n/a	n/a
21	JUND	chr1:153581318-153582045	HepG2	liver:	n/a	n/a
22	FOXA1	chr1:153581125-153581565	T-47D	breast:	n/a	n/a
23	ZBTB7A	chr1:153581294-153581566	HepG2	liver:	n/a	n/a
24	JUND	chr1:153581287-153582191	HepG2	liver:	n/a	n/a
25	POLR2A	chr1:153580458-153582090	ECC-1	luminal epithelium:	n/a	n/a
26	EP300	chr1:153580431-153582499	MCF-7	breast:	n/a	chr1:153580785-153580799
27	PBX3	chr1:153581205-153582163	A549	lung:	n/a	chr1:153581853-153581862
28	POLR2A	chr1:153581091-153584061	Hela-S3	cervix:	n/a	n/a
29	TAF1	chr1:153581268-153581626	SK-N-SH	brain:	n/a	n/a
30	SP1	chr1:153581049-153582298	A549	lung:	n/a	chr1:153581868-153581878 chr1:153581868-153581877 chr1:153581879-153581889 chr1:153581832-153581846
31	CEBPB	chr1:153581244-153581544	HepG2	liver:	n/a	n/a
32	TCF12	chr1:153580463-153581888	ECC-1	luminal epithelium:	n/a	chr1:153581050-153581060 chr1:153581524-153581534 chr1:153581015-153581022 chr1:153580817-153580825
33	TAF1	chr1:153581283-153582058	Hela-S3	cervix:	n/a	n/a
34	EGR1	chr1:153580530-153582198	MCF-7	breast:	n/a	chr1:153581357-153581368 chr1:153581351-153581366
35	POLR2A	chr1:153580843-153582539	U87	brain:	n/a	n/a
36	MAX	chr1:153580951-153582503	A549	lung:	n/a	n/a
37	POLR2A	chr1:153581118-153584087	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr1:153581126-153582325	HCT-116	colon:	n/a	n/a
39	TCF12	chr1:153581063-153583011	A549	lung:	n/a	chr1:153581524-153581534
40	TFAP2C	chr1:153580662-153582263	Hela-S3	cervix:	n/a	chr1:153580896-153580911
41	HNF4A	chr1:153581179-153581643	HepG2	liver:	n/a	chr1:153581232-153581247 chr1:153581233-153581245 chr1:153581232-153581247 chr1:153581228-153581250 chr1:153581413-153581428 chr1:153581233-153581245 chr1:153581232-153581247
42	MXI1	chr1:153580964-153582308	HepG2	liver:	n/a	n/a
43	GATA3	chr1:153581021-153582062	A549	lung:	n/a	chr1:153581551-153581560
44	NR2F2	chr1:153580519-153582242	MCF-7	breast:	n/a	n/a
45	MAFK	chr1:153581236-153582034	Hela-S3	cervix:	n/a	n/a
46	FOSL2	chr1:153580567-153582134	MCF-7	breast:	n/a	n/a
47	HA-E2F1	chr1:153580967-153581689	MCF-7	breast:	n/a	n/a
48	POLR2A	chr1:153578024-153582691	HUVEC	blood vessel:	n/a	n/a
49	HDAC2	chr1:153580228-153582222	MCF-7	breast:	n/a	chr1:153581238-153581246
50	SMARCC2	chr1:153581117-153583552	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153507285..153510261-chr1:153579792..153582160,3	MCF-7	breast:
2	chr1:153581285..153583404-chr1:153640253..153643290,3	MCF-7	breast:
3	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
4	chr1:153581196..153582723-chr8:22366793..22368546,2	MCF-7	breast:
5	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
6	chr1:153580730..153582256-chr1:153699773..153701811,2	MCF-7	breast:
7	chr1:153580088..153583370-chr1:153747776..153750328,4	MCF-7	breast:
8	chr1:153579256..153583611-chr1:153630358..153635573,4	MCF-7	breast:
9	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
10	chr1:153515934..153518266-chr1:153581311..153583180,3	MCF-7	breast:
11	chr1:153519598..153522352-chr1:153580214..153582486,2	K562	blood:
12	chr1:153539321..153541162-chr1:153580987..153583409,2	K562	blood:
13	chr1:153507840..153508475-chr1:153581398..153581986,2	Hela-S3	cervix:

Variant related genes	Relation type
S100A16	TF binding region
ENSG00000143624	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000188015	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000197956	Chromatin interaction
ENSG00000120910	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[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28444667	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]
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:97 , 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	chr1:153579800-153581600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:153579800-153583000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:153579800-153583600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:153580000-153581600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
9	chr1:153580200-153581600	Enhancers	Stomach Mucosa	stomach
10	chr1:153580200-153584800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:153580400-153581800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:153580400-153581800	Weak transcription	Aorta	Aorta
13	chr1:153580400-153582000	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr1:153580400-153582200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:153580400-153582800	Transcr. at gene 5' and 3'	NHLF	lung
16	chr1:153580400-153583200	Transcr. at gene 5' and 3'	NHEK	skin
17	chr1:153580600-153581600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr1:153580600-153581800	Active TSS	Fetal Kidney	kidney
19	chr1:153580600-153581800	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr1:153580600-153581800	Flanking Active TSS	Placenta	Placenta
21	chr1:153580600-153581800	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
22	chr1:153580600-153582000	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr1:153580600-153582000	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr1:153580600-153582000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr1:153580600-153582000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
26	chr1:153580600-153582200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:153580600-153582200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:153580600-153582200	Flanking Active TSS	Brain Cingulate Gyrus	brain
29	chr1:153580600-153582200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr1:153580600-153582400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:153580600-153582400	Flanking Active TSS	NH-A	brain
32	chr1:153580600-153583200	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr1:153580600-153583600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:153580800-153581600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr1:153580800-153581600	Active TSS	Right Ventricle	heart
36	chr1:153580800-153581800	Flanking Active TSS	Fetal Muscle Trunk	muscle
37	chr1:153580800-153581800	Active TSS	Rectal Smooth Muscle	rectum
38	chr1:153580800-153582000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:153580800-153582000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr1:153580800-153582000	Active TSS	HSMMtube	muscle
41	chr1:153580800-153582400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr1:153580800-153582600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:153580800-153582600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr1:153580800-153582800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:153580800-153582800	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr1:153580800-153583000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr1:153580800-153583200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:153580800-153583200	Flanking Active TSS	Colonic Mucosa	Colon
49	chr1:153580800-153583600	Flanking Active TSS	Osteobl	bone
50	chr1:153581000-153581600	Enhancers	HUES48 Cell Line	embryonic stem cell

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