Variant report

Variant	rs7511890
Chromosome Location	chr1:94050864-94050865
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	GATA3	chr1:94050475-94051214	A549	lung:	n/a	chr1:94051020-94051030 chr1:94051023-94051030 chr1:94051019-94051035 chr1:94051023-94051030 chr1:94051023-94051030 chr1:94051016-94051037
2	POLR2A	chr1:94050614-94050969	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:94050773-94051042	ECC-1	luminal epithelium:	n/a	chr1:94050985-94051000
4	ARID3A	chr1:94050801-94051111	HepG2	liver:	n/a	n/a
5	MYC	chr1:94050626-94050946	MCF-7	breast:	n/a	n/a
6	POLR2A	chr1:94050625-94050876	Hela-S3	cervix:	n/a	n/a
7	GATA3	chr1:94050518-94051268	MCF-7	breast:	n/a	chr1:94051020-94051030 chr1:94051023-94051030 chr1:94051019-94051035 chr1:94051023-94051030 chr1:94051023-94051030 chr1:94051016-94051037
8	USF2	chr1:94050427-94051207	Hela-S3	cervix:	n/a	n/a
9	ZNF217	chr1:94050544-94051070	MCF-7	breast:	n/a	n/a
10	FOS	chr1:94050776-94050940	MCF10A-Er-Src	breast:	n/a	n/a
11	EP300	chr1:94050724-94050976	HepG2	liver:	n/a	n/a
12	TCF12	chr1:94050553-94051345	MCF-7	breast:	n/a	chr1:94050848-94050858 chr1:94050791-94050801
13	FOSL2	chr1:94050570-94051085	A549	lung:	n/a	n/a
14	POLR2A	chr1:94050567-94050915	A549	lung:	n/a	n/a
15	YY1	chr1:94050583-94051085	ECC-1	luminal epithelium:	n/a	chr1:94050860-94050879 chr1:94050865-94050873 chr1:94050843-94050854
16	YY1	chr1:94050603-94051059	ECC-1	luminal epithelium:	n/a	chr1:94050860-94050879 chr1:94050865-94050873 chr1:94050843-94050854
17	EP300	chr1:94050530-94051249	A549	lung:	n/a	chr1:94051016-94051030
18	GATA3	chr1:94050550-94051133	T-47D	breast:	n/a	chr1:94051020-94051030 chr1:94051023-94051030 chr1:94051019-94051035 chr1:94051023-94051030 chr1:94051023-94051030 chr1:94051016-94051037
19	NR3C1	chr1:94050605-94051142	A549	lung:	n/a	n/a
20	POLR2A	chr1:94050248-94051202	HepG2	liver:	n/a	n/a
21	SP1	chr1:94050503-94051328	A549	lung:	n/a	chr1:94050838-94050851
22	GATA3	chr1:94050462-94051159	T-47D	breast:	n/a	chr1:94051020-94051030 chr1:94051023-94051030 chr1:94051019-94051035 chr1:94051023-94051030 chr1:94051023-94051030 chr1:94051016-94051037
23	SMC3	chr1:94050863-94050986	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:94050505-94051175	Hela-S3	cervix:	n/a	n/a
25	CEBPB	chr1:94050658-94050901	Hela-S3	cervix:	n/a	n/a
26	MAX	chr1:94050475-94051174	ECC-1	luminal epithelium:	n/a	n/a
27	TEAD4	chr1:94050592-94051023	MCF-7	breast:	n/a	n/a
28	TCF12	chr1:94050330-94051340	A549	lung:	n/a	chr1:94050848-94050858 chr1:94050791-94050801
29	FOSL2	chr1:94050550-94051069	HepG2	liver:	n/a	n/a
30	TCF12	chr1:94050543-94051233	ECC-1	luminal epithelium:	n/a	chr1:94050848-94050858 chr1:94050791-94050801
31	SP1	chr1:94050661-94051252	HepG2	liver:	n/a	chr1:94050838-94050851
32	TCF12	chr1:94050543-94051204	ECC-1	luminal epithelium:	n/a	chr1:94050848-94050858 chr1:94050791-94050801
33	NR3C1	chr1:94050623-94051092	A549	lung:	n/a	n/a
34	NR3C1	chr1:94050597-94051154	A549	lung:	n/a	n/a
35	HNF4G	chr1:94050669-94051113	HepG2	liver:	n/a	chr1:94050946-94050960
36	FOS	chr1:94050754-94050924	MCF10A-Er-Src	breast:	n/a	n/a
37	HDAC2	chr1:94050574-94051212	HepG2	liver:	n/a	n/a
38	EP300	chr1:94050673-94051192	HepG2	liver:	n/a	chr1:94051016-94051030
39	TCF12	chr1:94050651-94051132	A549	lung:	n/a	chr1:94050848-94050858 chr1:94050791-94050801
40	POLR2A	chr1:94050501-94050957	ECC-1	luminal epithelium:	n/a	n/a
41	STAT3	chr1:94050727-94050866	MCF10A-Er-Src	breast:	n/a	n/a
42	FOXA1	chr1:94050735-94051231	HepG2	liver:	n/a	chr1:94050985-94051000
43	RFX5	chr1:94050629-94050996	Hela-S3	cervix:	n/a	n/a
44	MAX	chr1:94050530-94051080	MCF-7	breast:	n/a	n/a
45	POLR2A	chr1:94050618-94050971	Hela-S3	cervix:	n/a	n/a
46	CHD2	chr1:94050671-94050979	Hela-S3	cervix:	n/a	n/a
47	CHD2	chr1:94050765-94050965	HepG2	liver:	n/a	n/a
48	USF1	chr1:94050644-94051091	A549	lung:	n/a	n/a
49	MAX	chr1:94050497-94051225	HepG2	liver:	n/a	n/a
50	JUND	chr1:94050768-94051029	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:93913254..93915566-chr1:94049347..94051024,2	MCF-7	breast:
2	chr1:94050731..94051289-chr1:94064727..94065318,2	MCF-7	breast:
3	chr1:94048472..94052407-chr1:94077212..94082015,4	MCF-7	breast:

Variant related genes	Relation type
BCAR3	TF binding region
ENSG00000137936	Chromatin interaction
ENSG00000137942	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11576435	1.00[ASN][1000 genomes]
rs11577352	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11579004	1.00[ASN][1000 genomes]
rs11579685	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580965	1.00[ASN][1000 genomes]
rs11588860	1.00[ASN][1000 genomes]
rs12066343	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12073093	1.00[ASN][1000 genomes]
rs12090736	1.00[ASN][1000 genomes]
rs12732557	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739747	1.00[ASN][1000 genomes]
rs12740779	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12744941	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12757325	1.00[ASN][1000 genomes]
rs12760092	1.00[ASN][1000 genomes]
rs17110063	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110101	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110111	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110225	1.00[ASN][1000 genomes]
rs17110370	1.00[ASN][1000 genomes]
rs1877603	1.00[ASN][1000 genomes]
rs1877604	1.00[ASN][1000 genomes]
rs1891138	1.00[ASN][1000 genomes]
rs2818163	1.00[ASN][1000 genomes]
rs34183660	1.00[ASN][1000 genomes]
rs34423897	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34663884	1.00[ASN][1000 genomes]
rs34666525	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34726063	1.00[ASN][1000 genomes]
rs35126293	1.00[ASN][1000 genomes]
rs35691338	1.00[ASN][1000 genomes]
rs35896714	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35972761	1.00[ASN][1000 genomes]
rs36115605	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3950119	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59996315	1.00[ASN][1000 genomes]
rs61780979	1.00[ASN][1000 genomes]
rs61780999	1.00[ASN][1000 genomes]
rs6660968	1.00[ASN][1000 genomes]
rs6666778	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677770	1.00[ASN][1000 genomes]
rs6679609	1.00[ASN][1000 genomes]
rs6683296	1.00[ASN][1000 genomes]
rs66966060	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67043929	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67300695	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67354439	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67511232	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71652539	1.00[ASN][1000 genomes]
rs72721041	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514579	0.83[EUR][1000 genomes]
rs7525880	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531106	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543098	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543734	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7543763	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553185	1.00[ASN][1000 genomes]
rs7555302	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761802	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 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	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
2	chr1:94031800-94052400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr1:94032000-94053600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:94038400-94054000	Weak transcription	Brain Substantia Nigra	brain
5	chr1:94038400-94054800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:94038600-94051800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:94038600-94054200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:94040000-94055000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:94041800-94059400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:94042000-94054800	Weak transcription	Primary B cells from cord blood	blood
11	chr1:94042200-94063200	Weak transcription	Brain Germinal Matrix	brain
12	chr1:94042800-94053000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:94043000-94058400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:94045400-94053600	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:94046000-94051600	Strong transcription	NH-A	brain
16	chr1:94046600-94058200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:94047000-94051200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:94047200-94051000	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr1:94047200-94053600	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr1:94047400-94051200	Genic enhancers	Fetal Muscle Leg	muscle
21	chr1:94047400-94053400	Strong transcription	HUVEC	blood vessel
22	chr1:94047600-94051400	Genic enhancers	Placenta	Placenta
23	chr1:94048200-94052000	Weak transcription	Fetal Lung	lung
24	chr1:94048200-94054600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:94048200-94059200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:94048200-94059400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:94048400-94051000	Active TSS	Colonic Mucosa	Colon
28	chr1:94048400-94053200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:94048400-94059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:94048600-94064200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr1:94048800-94052200	Genic enhancers	NHDF-Ad	bronchial
32	chr1:94048800-94053800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:94049000-94051800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:94049000-94052000	Genic enhancers	Adipose Nuclei	Adipose
35	chr1:94049400-94051400	Genic enhancers	HSMM	muscle
36	chr1:94049400-94051800	Genic enhancers	Osteobl	bone
37	chr1:94049400-94052200	Genic enhancers	Hela-S3	cervix
38	chr1:94049600-94051000	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr1:94049600-94051400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:94049600-94051400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:94049600-94051600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:94049600-94051800	Weak transcription	Lung	lung
43	chr1:94049600-94052600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:94049600-94053600	Enhancers	Fetal Heart	heart
45	chr1:94049600-94059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:94049800-94051200	Enhancers	Colon Smooth Muscle	Colon
47	chr1:94049800-94051200	Enhancers	Fetal Kidney	kidney
48	chr1:94049800-94052000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:94049800-94052600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:94049800-94052600	Genic enhancers	HMEC	breast

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