Variant report

Variant	rs9660389
Chromosome Location	chr1:153582067-153582068
allele	A/G
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	EP300	chr1:153580489-153582132	ECC-1	luminal epithelium:	n/a	chr1:153580785-153580799
3	PBX3	chr1:153581146-153582234	SK-N-SH	brain:	n/a	chr1:153581853-153581862
4	POLR2A	chr1:153580416-153585950	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:153581191-153582124	HepG2	liver:	n/a	n/a
6	TBL1XR1	chr1:153581733-153582231	K562	blood:	n/a	n/a
7	POLR2A	chr1:153580558-153582260	HepG2	liver:	n/a	n/a
8	MAX	chr1:153581311-153582177	K562	blood:	n/a	n/a
9	MYC	chr1:153581252-153582210	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:153581108-153582142	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:153578800-153582876	HUVEC	blood vessel:	n/a	n/a
12	JUND	chr1:153581287-153582191	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:153580458-153582090	ECC-1	luminal epithelium:	n/a	n/a
14	TBP	chr1:153581728-153582068	K562	blood:	n/a	n/a
15	EP300	chr1:153580431-153582499	MCF-7	breast:	n/a	chr1:153580785-153580799
16	PBX3	chr1:153581205-153582163	A549	lung:	n/a	chr1:153581853-153581862
17	POLR2A	chr1:153581091-153584061	Hela-S3	cervix:	n/a	n/a
18	MYC	chr1:153581570-153582262	K562	blood:	n/a	n/a
19	CUX1	chr1:153581939-153582499	K562	blood:	n/a	n/a
20	SP1	chr1:153581049-153582298	A549	lung:	n/a	chr1:153581868-153581878 chr1:153581868-153581877 chr1:153581879-153581889 chr1:153581832-153581846
21	EGR1	chr1:153580530-153582198	MCF-7	breast:	n/a	chr1:153581357-153581368 chr1:153581351-153581366
22	POLR2A	chr1:153580843-153582539	U87	brain:	n/a	n/a
23	MAX	chr1:153580951-153582503	A549	lung:	n/a	n/a
24	POLR2A	chr1:153581118-153584087	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:153581126-153582325	HCT-116	colon:	n/a	n/a
26	TCF12	chr1:153581063-153583011	A549	lung:	n/a	chr1:153581524-153581534
27	TFAP2C	chr1:153580662-153582263	Hela-S3	cervix:	n/a	chr1:153580896-153580911
28	TBL1XR1	chr1:153581871-153582295	K562	blood:	n/a	n/a
29	HMGN3	chr1:153581732-153582144	K562	blood:	n/a	n/a
30	MXI1	chr1:153580964-153582308	HepG2	liver:	n/a	n/a
31	HDAC2	chr1:153581658-153582119	HepG2	liver:	n/a	n/a
32	NR2F2	chr1:153580519-153582242	MCF-7	breast:	n/a	n/a
33	FOSL2	chr1:153580567-153582134	MCF-7	breast:	n/a	n/a
34	POLR2A	chr1:153578024-153582691	HUVEC	blood vessel:	n/a	n/a
35	HDAC2	chr1:153580228-153582222	MCF-7	breast:	n/a	chr1:153581238-153581246
36	SMARCC2	chr1:153581117-153583552	Hela-S3	cervix:	n/a	n/a
37	BHLHE40	chr1:153581110-153582092	HepG2	liver:	n/a	chr1:153581428-153581444
38	POLR2A	chr1:153581241-153582106	A549	lung:	n/a	n/a
39	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
40	POLR2A	chr1:153581218-153582091	PANC-1	pancreas:	n/a	n/a
41	EP300	chr1:153581752-153582153	K562	blood:	n/a	n/a
42	EGR1	chr1:153580500-153582254	MCF-7	breast:	n/a	chr1:153581357-153581368 chr1:153581351-153581366
43	HNF4A	chr1:153580812-153582281	HepG2	liver:	n/a	chr1:153581905-153581918 chr1:153581232-153581247 chr1:153581233-153581245 chr1:153581900-153581916 chr1:153581232-153581247 chr1:153581228-153581250 chr1:153581904-153581911 chr1:153581831-153581853 chr1:153581413-153581428 chr1:153581233-153581245 chr1:153581232-153581247 chr1:153581905-153581918
44	MXI1	chr1:153581137-153582130	Hela-S3	cervix:	n/a	n/a
45	MYC	chr1:153581286-153582241	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr1:153578145-153583129	HUVEC	blood vessel:	n/a	n/a
47	TBP	chr1:153581228-153582086	Hela-S3	cervix:	n/a	n/a
48	RCOR1	chr1:153580335-153582657	IMR90	lung:	n/a	n/a
49	POLR2A	chr1:153580439-153582139	HUVEC	blood vessel:	n/a	n/a
50	IRF1	chr1:153581729-153582214	K562	blood:	n/a	chr1:153581876-153581890

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	chr1:153581957..153582462-chr1:153739464..153739964,2	Hela-S3	cervix:

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

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs6688800	1.00[ASN][1000 genomes]
rs73009954	1.00[ASN][1000 genomes]
rs9660416	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9728059	0.82[EUR][1000 genomes]
rs9728400	0.85[EUR][1000 genomes];1.00[ASN][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:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153577800-153582800	Weak transcription	Small Intestine	intestine
2	chr1:153578800-153584800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:153579400-153583600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:153579800-153583000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:153579800-153583600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:153580200-153584800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:153580400-153582200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:153580400-153582800	Transcr. at gene 5' and 3'	NHLF	lung
9	chr1:153580400-153583200	Transcr. at gene 5' and 3'	NHEK	skin
10	chr1:153580600-153582200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:153580600-153582200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:153580600-153582200	Flanking Active TSS	Brain Cingulate Gyrus	brain
13	chr1:153580600-153582200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr1:153580600-153582400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:153580600-153582400	Flanking Active TSS	NH-A	brain
16	chr1:153580600-153583200	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr1:153580600-153583600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:153580800-153582400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr1:153580800-153582600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:153580800-153582600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr1:153580800-153582800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:153580800-153582800	Flanking Active TSS	Brain Substantia Nigra	brain
23	chr1:153580800-153583000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr1:153580800-153583200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:153580800-153583200	Flanking Active TSS	Colonic Mucosa	Colon
26	chr1:153580800-153583600	Flanking Active TSS	Osteobl	bone
27	chr1:153581000-153582200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:153581000-153582400	Flanking Active TSS	Hela-S3	cervix
29	chr1:153581000-153583200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:153581000-153583400	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr1:153581000-153584000	Enhancers	Colon Smooth Muscle	Colon
32	chr1:153581000-153584200	Enhancers	Fetal Lung	lung
33	chr1:153581200-153582200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr1:153581200-153582400	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr1:153581200-153582600	Enhancers	H9 Cell Line	embryonic stem cell
36	chr1:153581200-153584200	Enhancers	Gastric	stomach
37	chr1:153581200-153584200	Enhancers	Pancreas	Pancrea
38	chr1:153581400-153582200	Weak transcription	Psoas Muscle	Psoas
39	chr1:153581400-153582400	Flanking Active TSS	K562	blood
40	chr1:153581400-153583600	Enhancers	Ovary	ovary
41	chr1:153581400-153584200	Enhancers	Left Ventricle	heart
42	chr1:153581400-153584800	Enhancers	Fetal Heart	heart
43	chr1:153581600-153582200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr1:153581600-153582200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:153581600-153582400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:153581600-153582400	Flanking Active TSS	Stomach Mucosa	stomach
47	chr1:153581600-153582400	Flanking Active TSS	HSMM	muscle
48	chr1:153581600-153582600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:153581600-153582800	Enhancers	Placenta Amnion	Placenta Amnion
50	chr1:153581600-153583000	Transcr. at gene 5' and 3'	Esophagus	oesophagus

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