Variant report

Variant	rs9660416
Chromosome Location	chr1:153582264-153582265
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	POLR2A	chr1:153580416-153585950	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:153578800-153582876	HUVEC	blood vessel:	n/a	n/a
4	EP300	chr1:153580431-153582499	MCF-7	breast:	n/a	chr1:153580785-153580799
5	POLR2A	chr1:153581091-153584061	Hela-S3	cervix:	n/a	n/a
6	CUX1	chr1:153581939-153582499	K562	blood:	n/a	n/a
7	SP1	chr1:153581049-153582298	A549	lung:	n/a	chr1:153581868-153581878 chr1:153581868-153581877 chr1:153581879-153581889 chr1:153581832-153581846
8	POLR2A	chr1:153580843-153582539	U87	brain:	n/a	n/a
9	MAX	chr1:153580951-153582503	A549	lung:	n/a	n/a
10	POLR2A	chr1:153581118-153584087	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:153581126-153582325	HCT-116	colon:	n/a	n/a
12	TCF12	chr1:153581063-153583011	A549	lung:	n/a	chr1:153581524-153581534
13	TBL1XR1	chr1:153581871-153582295	K562	blood:	n/a	n/a
14	MXI1	chr1:153580964-153582308	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:153578024-153582691	HUVEC	blood vessel:	n/a	n/a
16	SMARCC2	chr1:153581117-153583552	Hela-S3	cervix:	n/a	n/a
17	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
18	POLR2A	chr1:153578145-153583129	HUVEC	blood vessel:	n/a	n/a
19	RCOR1	chr1:153580335-153582657	IMR90	lung:	n/a	n/a
20	CHD2	chr1:153581214-153582382	Hela-S3	cervix:	n/a	n/a
21	BHLHE40	chr1:153581284-153582443	K562	blood:	n/a	chr1:153581428-153581444
22	CEBPB	chr1:153581208-153582322	Hela-S3	cervix:	n/a	n/a
23	EP300	chr1:153581114-153582288	HepG2	liver:	n/a	n/a
24	CEBPB	chr1:153581827-153582297	K562	blood:	n/a	n/a
25	MAZ	chr1:153580631-153582545	IMR90	lung:	n/a	n/a
26	SIN3AK20	chr1:153580199-153582486	MCF-7	breast:	n/a	n/a
27	UBTF	chr1:153581828-153582381	K562	blood:	n/a	n/a
28	POLR2A	chr1:153580980-153582424	HepG2	liver:	n/a	n/a
29	NR2F2	chr1:153580506-153582314	MCF-7	breast:	n/a	n/a
30	POLR2A	chr1:153580356-153583237	HepG2	liver:	n/a	n/a
31	SMC3	chr1:153581080-153582354	Hela-S3	cervix:	n/a	chr1:153582313-153582321
32	GATA2	chr1:153581193-153583269	HUVEC	blood vessel:	n/a	chr1:153581551-153581560 chr1:153582836-153582846
33	FOSL2	chr1:153581035-153582533	A549	lung:	n/a	n/a
34	MAZ	chr1:153581690-153582415	K562	blood:	n/a	n/a
35	ZNF384	chr1:153581859-153582283	K562	blood:	n/a	n/a
36	NR2F2	chr1:153581740-153582274	K562	blood:	n/a	n/a
37	POLR2A	chr1:153578333-153582858	HUVEC	blood vessel:	n/a	n/a
38	CEBPB	chr1:153581895-153582309	K562	blood:	n/a	n/a
39	SMARCC1	chr1:153580778-153586030	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr1:153581230-153582286	IMR90	lung:	n/a	n/a
41	POLR2A	chr1:153577237-153583097	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr1:153579147-153585872	U87	brain:	n/a	n/a
43	GATA3	chr1:153580371-153582479	MCF-7	breast:	n/a	chr1:153581551-153581560 chr1:153580779-153580789
44	RCOR1	chr1:153581745-153582517	K562	blood:	n/a	n/a
45	JUND	chr1:153581378-153582350	K562	blood:	n/a	n/a
46	POLR2A	chr1:153580843-153582511	U87	brain:	n/a	n/a
47	CEBPB	chr1:153581781-153582369	HepG2	liver:	n/a	n/a
48	TEAD4	chr1:153581552-153582356	K562	blood:	n/a	chr1:153581628-153581637
49	EGR1	chr1:153581705-153582315	K562	blood:	n/a	n/a
50	MAX	chr1:153580226-153582521	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153581723..153582287-chr11:62521134..62521681,2	Hela-S3	cervix:
2	chr1:153581285..153583404-chr1:153640253..153643290,3	MCF-7	breast:
3	chr1:153581620..153582323-chr17:62223043..62223818,2	Hela-S3	cervix:
4	chr1:153580618..153585586-chr1:153936399..153942199,7	MCF-7	breast:
5	chr1:153581196..153582723-chr8:22366793..22368546,2	MCF-7	breast:
6	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
7	chr1:153518244..153520896-chr1:153581745..153584776,3	MCF-7	breast:
8	chr1:153581488..153584174-chr1:153940194..153943077,2	MCF-7	breast:
9	chr1:153580088..153583370-chr1:153747776..153750328,4	MCF-7	breast:
10	chr1:153579256..153583611-chr1:153630358..153635573,4	MCF-7	breast:
11	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
12	chr1:153515934..153518266-chr1:153581311..153583180,3	MCF-7	breast:
13	chr1:153519598..153522352-chr1:153580214..153582486,2	K562	blood:
14	chr1:153539321..153541162-chr1:153580987..153583409,2	K562	blood:
15	chr1:153325873..153327403-chr1:153582234..153585086,2	MCF-7	breast:
16	chr1:153581957..153582462-chr1:153739464..153739964,2	Hela-S3	cervix:

Variant related genes	Relation type
S100A16	TF binding region
ENSG00000273026	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000120910	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000188015	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000185670	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000266402	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]
rs9660389	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9728059	0.82[EUR][1000 genomes]
rs9728400	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];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	chr1:153580400-153582800	Transcr. at gene 5' and 3'	NHLF	lung
8	chr1:153580400-153583200	Transcr. at gene 5' and 3'	NHEK	skin
9	chr1:153580600-153582400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr1:153580600-153582400	Flanking Active TSS	NH-A	brain
11	chr1:153580600-153583200	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr1:153580600-153583600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:153580800-153582400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr1:153580800-153582600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:153580800-153582600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:153580800-153582800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:153580800-153582800	Flanking Active TSS	Brain Substantia Nigra	brain
18	chr1:153580800-153583000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
19	chr1:153580800-153583200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:153580800-153583200	Flanking Active TSS	Colonic Mucosa	Colon
21	chr1:153580800-153583600	Flanking Active TSS	Osteobl	bone
22	chr1:153581000-153582400	Flanking Active TSS	Hela-S3	cervix
23	chr1:153581000-153583200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:153581000-153583400	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr1:153581000-153584000	Enhancers	Colon Smooth Muscle	Colon
26	chr1:153581000-153584200	Enhancers	Fetal Lung	lung
27	chr1:153581200-153582400	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr1:153581200-153582600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr1:153581200-153584200	Enhancers	Gastric	stomach
30	chr1:153581200-153584200	Enhancers	Pancreas	Pancrea
31	chr1:153581400-153582400	Flanking Active TSS	K562	blood
32	chr1:153581400-153583600	Enhancers	Ovary	ovary
33	chr1:153581400-153584200	Enhancers	Left Ventricle	heart
34	chr1:153581400-153584800	Enhancers	Fetal Heart	heart
35	chr1:153581600-153582400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:153581600-153582400	Flanking Active TSS	Stomach Mucosa	stomach
37	chr1:153581600-153582400	Flanking Active TSS	HSMM	muscle
38	chr1:153581600-153582600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:153581600-153582800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr1:153581600-153583000	Transcr. at gene 5' and 3'	Esophagus	oesophagus
41	chr1:153581600-153583200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr1:153581600-153583200	Flanking Active TSS	HMEC	breast
43	chr1:153581600-153584000	Enhancers	Spleen	Spleen
44	chr1:153581800-153582400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:153581800-153582400	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr1:153581800-153582400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:153581800-153582400	Flanking Active TSS	Rectal Smooth Muscle	rectum
48	chr1:153581800-153582600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr1:153581800-153582800	Genic enhancers	Fetal Stomach	stomach
50	chr1:153581800-153582800	Flanking Active TSS	HUVEC	blood vessel

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