Variant report

Variant	rs9887866
Chromosome Location	chr1:150039267-150039268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:407)
CpG islands
(count:0)
Chromatin interactive
region (count:33)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:407 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr1:150038846-150040252	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr1:150038902-150040252	A549	lung:	n/a	n/a
3	CEBPB	chr1:150038855-150040183	MCF-7	breast:	n/a	chr1:150039333-150039344 chr1:150039332-150039345
4	EP300	chr1:150039177-150040075	Hela-S3	cervix:	n/a	chr1:150039681-150039697
5	POLR2A	chr1:150039015-150040189	HUVEC	blood vessel:	n/a	n/a
6	ELK1	chr1:150039175-150040005	GM12878	blood:	n/a	n/a
7	CHD2	chr1:150039002-150040065	HepG2	liver:	n/a	n/a
8	SIN3AK20	chr1:150038769-150040371	MCF-7	breast:	n/a	n/a
9	POLR2A	chr1:150038914-150040060	GM18526	blood:	n/a	n/a
10	POLR2A	chr1:150039057-150040154	U87	brain:	n/a	n/a
11	MTA3	chr1:150038755-150040273	GM12878	blood:	n/a	n/a
12	CTCF	chr1:150039260-150039410	HCFaa	heart:	n/a	n/a
13	TBP	chr1:150038894-150040038	H1-hESC	embryonic stem cell:	n/a	n/a
14	YY1	chr1:150039256-150040142	GM12892	blood:	n/a	n/a
15	ARID3A	chr1:150039088-150040025	K562	blood:	n/a	n/a
16	MXI1	chr1:150039208-150040118	H1-hESC	embryonic stem cell:	n/a	n/a
17	GATA3	chr1:150038896-150040216	A549	lung:	n/a	n/a
18	POLR2A	chr1:150038871-150040023	K562	blood:	n/a	n/a
19	STAT5A	chr1:150039129-150040397	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:150038780-150040141	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr1:150038903-150040062	GM15510	blood:	n/a	n/a
22	POLR2A	chr1:150038815-150040110	Hela-S3	cervix:	n/a	n/a
23	MAX	chr1:150038922-150040254	MCF-7	breast:	n/a	chr1:150039085-150039095 chr1:150039683-150039692 chr1:150039383-150039390
24	CTCF	chr1:150039180-150039330	HMEC	breast:	n/a	n/a
25	SIN3AK20	chr1:150038703-150040364	HCT-116	colon:	n/a	n/a
26	PML	chr1:150038634-150040284	GM12878	blood:	n/a	n/a
27	E2F6	chr1:150039152-150039659	K562	blood:	n/a	n/a
28	MYBL2	chr1:150038818-150040048	HepG2	liver:	n/a	n/a
29	RELA	chr1:150039254-150040049	GM19193	blood:	n/a	n/a
30	POLR2A	chr1:150038875-150040086	Raji	blood:	n/a	n/a
31	HEY1	chr1:150039187-150040067	K562	blood:	n/a	n/a
32	POLR2A	chr1:150038716-150040208	GM12892	blood:	n/a	n/a
33	REST	chr1:150038661-150040208	A549	lung:	n/a	chr1:150040182-150040195
34	POLR2A	chr1:150039058-150040095	GM12892	blood:	n/a	n/a
35	POLR2A	chr1:150039015-150040000	A549	lung:	n/a	n/a
36	JUND	chr1:150039147-150039895	A549	lung:	n/a	n/a
37	POLR2A	chr1:150038675-150040176	GM12892	blood:	n/a	n/a
38	ZNF143	chr1:150039067-150040040	Hela-S3	cervix:	n/a	chr1:150039765-150039783 chr1:150039339-150039358 chr1:150039767-150039776 chr1:150039765-150039774
39	HCFC1	chr1:150038434-150041146	Hela-S3	cervix:	n/a	n/a
40	ZKSCAN1	chr1:150038912-150040024	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr1:150038757-150040099	Hela-S3	cervix:	n/a	n/a
42	EP300	chr1:150038797-150040206	ECC-1	luminal epithelium:	n/a	chr1:150039681-150039697
43	E2F6	chr1:150038936-150040073	A549	lung:	n/a	chr1:150038936-150038953 chr1:150039090-150039099
44	POLR2A	chr1:150038777-150040296	SK-N-MC	brain:	n/a	n/a
45	MYC	chr1:150039133-150039948	MCF10A-Er-Src	breast:	n/a	chr1:150039683-150039692 chr1:150039383-150039390
46	MXI1	chr1:150038828-150040296	GM12878	blood:	n/a	n/a
47	JUND	chr1:150039141-150039738	HepG2	liver:	n/a	n/a
48	GABPA	chr1:150039050-150040285	SK-N-SH	brain:	n/a	chr1:150039090-150039099
49	ZBTB7A	chr1:150038965-150039362	HepG2	liver:	n/a	n/a
50	YY1	chr1:150039259-150040090	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:33 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150035483..150047454-chr1:150129931..150138567,28	MCF-7	breast:
2	chr1:150039161..150039812-chr7:141437730..141438529,2	Hela-S3	cervix:
3	chr1:149908339..149915829-chr1:150035449..150039990,12	MCF-7	breast:
4	chr1:149897261..149900212-chr1:150037388..150039333,2	MCF-7	breast:
5	chr1:149898324..149902062-chr1:150037827..150040253,4	MCF-7	breast:
6	chr1:150038862..150039533-chr5:177630955..177631779,2	Hela-S3	cervix:
7	chr1:149870325..149872593-chr1:150038343..150041327,5	MCF-7	breast:
8	chr1:149907171..149915966-chr1:150036158..150043011,15	MCF-7	breast:
9	chr1:150038609..150041088-chr1:150047588..150050887,5	MCF-7	breast:
10	chr1:149887372..149890270-chr1:150038277..150040305,2	K562	blood:
11	chr1:149900549..149903702-chr1:150037332..150040713,4	MCF-7	breast:
12	chr1:150038831..150039716-chr6:5260490..5261436,2	Hela-S3	cervix:
13	chr1:149855827..149861924-chr1:150032527..150042362,32	MCF-7	breast:
14	chr1:149817827..149821431-chr1:150036446..150041414,4	K562	blood:
15	chr1:149854948..149862391-chr1:150036900..150043965,32	MCF-7	breast:
16	chr1:150038983..150041057-chr1:150046382..150049857,3	MCF-7	breast:
17	chr1:149982208..149982928-chr1:150038867..150039793,2	MCF-7	breast:
18	chr1:149855739..149860992-chr1:150036779..150042618,12	K562	blood:
19	chr1:149897900..149900101-chr1:150038034..150041085,3	K562	blood:
20	chr1:150038076..150040720-chr1:150121290..150124944,3	K562	blood:
21	chr1:150037974..150040351-chr1:151020175..151022098,2	MCF-7	breast:
22	chr1:150039144..150039849-chr14:54907595..54908224,2	Hela-S3	cervix:
23	chr1:149982316..149983111-chr1:150039258..150039856,2	MCF-7	breast:
24	chr1:150038726..150039642-chr14:75744872..75745736,2	Hela-S3	cervix:
25	chr1:149977821..149984701-chr1:150037094..150041280,13	MCF-7	breast:
26	chr1:149814583..149816442-chr1:150038342..150040815,2	MCF-7	breast:
27	chr1:150038270..150039782-chr1:150120828..150123212,2	MCF-7	breast:
28	chr1:149818728..149822581-chr1:150037464..150041088,4	MCF-7	breast:
29	chr1:149855739..149863622-chr1:150034266..150042059,13	K562	blood:
30	chr1:150039197..150040027-chr20:42838795..42839496,2	Hela-S3	cervix:
31	chr1:149980215..149984264-chr1:150036474..150041542,10	K562	blood:
32	chr1:150039196..150039749-chr6:133135355..133136176,2	Hela-S3	cervix:
33	chr1:22379092..22379636-chr1:150039075..150039783,2	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OTUD7B-2	chr1:150035352-150039341	NONHSAT006267

No data

Variant related genes	Relation type
VPS45	TF binding region
ENSG00000197451	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000100528	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000106028	Chromatin interaction
ENSG00000159164	Chromatin interaction
ENSG00000145982	Chromatin interaction
ENSG00000214113	Chromatin interaction
ENSG00000203819	Chromatin interaction
ENSG00000228775	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000112306	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000261716	Chromatin interaction
ENSG00000143443	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000014914	Chromatin interaction
ENSG00000132823	Chromatin interaction
ENSG00000163113	Chromatin interaction
ENSG00000070831	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000220323	Chromatin interaction
ENSG00000143368	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10788868	1.00[MEX][hapmap]
rs11205325	1.00[MEX][hapmap];0.84[MKK][hapmap]
rs11205327	1.00[MEX][hapmap]
rs11205328	1.00[MEX][hapmap];0.84[MKK][hapmap]
rs6681679	0.84[MKK][hapmap]
rs6687257	1.00[MEX][hapmap];0.84[MKK][hapmap]
rs7517537	1.00[MEX][hapmap];0.84[MKK][hapmap]
rs7533714	0.87[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	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases
2	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 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	chr1:150037600-150040400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:150037800-150040800	Active TSS	K562	blood
3	chr1:150038000-150040200	Active TSS	Brain Angular Gyrus	brain
4	chr1:150038000-150040600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:150038000-150041200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:150038000-150041200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:150038200-150040000	Active TSS	HepG2	liver
8	chr1:150038200-150040400	Active TSS	Fetal Kidney	kidney
9	chr1:150038200-150040600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:150038200-150040600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:150038200-150040600	Active TSS	Fetal Brain Female	brain
12	chr1:150038200-150040600	Active TSS	NHLF	lung
13	chr1:150038400-150039400	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr1:150038400-150039400	Active TSS	Brain Germinal Matrix	brain
15	chr1:150038400-150040400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:150038400-150040400	Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr1:150038400-150040400	Active TSS	Fetal Heart	heart
18	chr1:150038400-150040600	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:150038400-150040600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:150038400-150040600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:150038400-150040600	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr1:150038400-150040600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:150038400-150040600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:150038400-150040600	Active TSS	Fetal Lung	lung
25	chr1:150038400-150040600	Active TSS	NH-A	brain
26	chr1:150038400-150040800	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:150038400-150040800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:150038400-150040800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:150038400-150040800	Active TSS	HSMMtube	muscle
30	chr1:150038400-150041000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:150038400-150041000	Active TSS	Stomach Smooth Muscle	stomach
32	chr1:150038400-150041200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr1:150038600-150039400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr1:150038600-150039400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:150038600-150039600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:150038600-150040400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:150038600-150040400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr1:150038600-150040400	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr1:150038600-150040400	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr1:150038600-150040400	Active TSS	Fetal Muscle Trunk	muscle
41	chr1:150038600-150040400	Active TSS	Hela-S3	cervix
42	chr1:150038600-150040600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr1:150038600-150040600	Active TSS	H1 Cell Line	embryonic stem cell
44	chr1:150038600-150040600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:150038600-150040600	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr1:150038600-150040600	Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:150038600-150040600	Active TSS	Brain Anterior Caudate	brain
48	chr1:150038600-150040600	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr1:150038600-150040600	Active TSS	Colon Smooth Muscle	Colon
50	chr1:150038600-150040600	Active TSS	Fetal Adrenal Gland	Adrenal Gland

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