Variant report

Variant	rs72480247
Chromosome Location	chr1:158969476-158969477
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	FOS	chr1:158969475-158971196	MCF10A-Er-Src	breast:	n/a	chr1:158970661-158970672
2	TAF1	chr1:158969309-158970011	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr1:158969453-158972350	MCF10A-Er-Src	breast:	n/a	n/a
4	BRCA1	chr1:158969378-158971208	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr1:158969414-158971012	MCF10A-Er-Src	breast:	n/a	chr1:158969771-158969779 chr1:158969771-158969794
6	STAT3	chr1:158969422-158971000	MCF10A-Er-Src	breast:	n/a	chr1:158969771-158969779 chr1:158969771-158969794
7	POLR2A	chr1:158969107-158970988	U87	brain:	n/a	n/a
8	YY1	chr1:158969406-158969886	H1-hESC	embryonic stem cell:	n/a	n/a
9	EP300	chr1:158969427-158969908	SK-N-SH_RA	brain:	n/a	n/a
10	CTCF	chr1:158969360-158969510	HMF	breast:	n/a	n/a
11	JUND	chr1:158969218-158969949	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:158969204-158971058	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr1:158969110-158970982	U87	brain:	n/a	n/a
14	MXI1	chr1:158969441-158970203	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr1:158969390-158969863	H1-hESC	embryonic stem cell:	n/a	n/a
16	TEAD4	chr1:158969429-158969998	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAZ	chr1:158968421-158970865	IMR90	lung:	n/a	n/a
18	KAP1	chr1:158969072-158970917	U2OS	brain:	n/a	n/a
19	SIN3A	chr1:158968579-158970048	H1-hESC	embryonic stem cell:	n/a	n/a
20	BACH1	chr1:158969462-158969881	H1-hESC	embryonic stem cell:	n/a	n/a
21	TBP	chr1:158969285-158969975	H1-hESC	embryonic stem cell:	n/a	n/a
22	EGR1	chr1:158969359-158969795	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr1:158969443-158970137	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:158969139-158970115	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr1:158969462-158970029	H1-hESC	embryonic stem cell:	n/a	n/a
26	E2F4	chr1:158969450-158969850	MCF10A-Er-Src	breast:	n/a	n/a
27	HDAC2	chr1:158969434-158969896	H1-hESC	embryonic stem cell:	n/a	n/a
28	YY1	chr1:158969357-158969985	SK-N-SH_RA	brain:	n/a	n/a
29	STAT1	chr1:158969159-158970848	Hela-S3	cervix:	n/a	chr1:158969771-158969779 chr1:158969769-158969780 chr1:158969771-158969794 chr1:158969282-158969294
30	FOS	chr1:158969473-158969980	MCF10A-Er-Src	breast:	n/a	n/a
31	YY1	chr1:158969383-158969992	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr1:158969422-158969817	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr1:158968441-158970901	MCF10A-Er-Src	breast:	n/a	n/a
34	FOXP2	chr1:158969449-158969880	SK-N-MC	brain:	n/a	n/a
35	MYC	chr1:158969371-158969851	H1-hESC	embryonic stem cell:	n/a	n/a
36	TFAP2A	chr1:158969351-158970090	Hela-S3	cervix:	n/a	chr1:158969493-158969505 chr1:158969636-158969651 chr1:158969493-158969505 chr1:158969493-158969505 chr1:158969493-158969505
37	CHD2	chr1:158969217-158970014	H1-hESC	embryonic stem cell:	n/a	n/a
38	KAP1	chr1:158969238-158970869	HEK293	kidney:	n/a	n/a
39	POLR2A	chr1:158969366-158969963	H1-hESC	embryonic stem cell:	n/a	n/a
40	EGR1	chr1:158969387-158969834	H1-hESC	embryonic stem cell:	n/a	n/a
41	STAT3	chr1:158968556-158971118	MCF10A-Er-Src	breast:	n/a	chr1:158969771-158969779 chr1:158969771-158969794 chr1:158969282-158969294
42	POLR2A	chr1:158968491-158970130	HUVEC	blood vessel:	n/a	n/a
43	ATF2	chr1:158969408-158969884	H1-hESC	embryonic stem cell:	n/a	n/a
44	MYC	chr1:158969354-158970077	MCF10A-Er-Src	breast:	n/a	n/a
45	CTBP2	chr1:158969464-158969922	H1-hESC	embryonic stem cell:	n/a	n/a
46	FOS	chr1:158969423-158971071	MCF10A-Er-Src	breast:	n/a	chr1:158970661-158970672
47	TCF12	chr1:158969313-158971025	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr1:158969232-158970222	U87	brain:	n/a	n/a
49	SP1	chr1:158969261-158970044	H1-hESC	embryonic stem cell:	n/a	n/a
50	SIN3AK20	chr1:158969444-158970095	PFSK-1	brain:	n/a	n/a

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1102013	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1102014	0.97[ASN][1000 genomes]
rs1102015	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1102016	0.82[ASN][1000 genomes]
rs11590737	0.94[ASN][1000 genomes]
rs12239437	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1578477	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1614568	0.95[ASN][1000 genomes]
rs1615480	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1623601	0.95[ASN][1000 genomes]
rs1772443	0.95[ASN][1000 genomes]
rs1935068	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1935070	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1935071	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2793856	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793857	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754464	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3754466	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3754467	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41264051	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56954127	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57218670	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57498847	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58506115	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58805430	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60086314	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60381726	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61254442	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71632651	0.99[ASN][1000 genomes]
rs72480244	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72480246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72480248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs856125	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856126	0.98[ASN][1000 genomes]
rs856127	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856131	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856132	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856133	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs856134	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs856135	0.82[ASN][1000 genomes]
rs856136	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs856140	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs856141	0.82[ASN][1000 genomes]
rs856142	0.82[ASN][1000 genomes]
rs860635	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002401	chr1:158712627-158972031	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	esv1793882	chr1:158961777-158972490	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv548043	chr1:158963127-158972490	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158960800-158975400	Weak transcription	Spleen	Spleen
2	chr1:158968400-158969600	Active TSS	Rectal Smooth Muscle	rectum
3	chr1:158968400-158969800	Active TSS	Fetal Kidney	kidney
4	chr1:158968400-158970200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr1:158968400-158970200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:158968400-158970200	Active TSS	Aorta	Aorta
7	chr1:158968400-158970200	Active TSS	Fetal Muscle Trunk	muscle
8	chr1:158968400-158970200	Active TSS	Psoas Muscle	Psoas
9	chr1:158968400-158970400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:158968400-158970400	Active TSS	Brain Anterior Caudate	brain
11	chr1:158968400-158970600	Active TSS	Brain Angular Gyrus	brain
12	chr1:158968400-158970600	Active TSS	Fetal Lung	lung
13	chr1:158968400-158970800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr1:158968400-158970800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:158968400-158970800	Active TSS	Fetal Brain Female	brain
16	chr1:158968400-158971000	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr1:158968400-158971000	Active TSS	Stomach Smooth Muscle	stomach
18	chr1:158968600-158969600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:158968600-158969600	Active TSS	Colonic Mucosa	Colon
20	chr1:158968600-158969800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:158968600-158969800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr1:158968600-158969800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:158968600-158969800	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr1:158968600-158969800	Active TSS	NHLF	lung
25	chr1:158968600-158970000	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr1:158968600-158970200	Active TSS	H1 Cell Line	embryonic stem cell
27	chr1:158968600-158970200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:158968600-158970200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:158968600-158970200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr1:158968600-158970200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:158968600-158970200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:158968600-158970200	Active TSS	Brain Substantia Nigra	brain
33	chr1:158968600-158970200	Active TSS	Duodenum Mucosa	Duodenum
34	chr1:158968600-158970200	Active TSS	Fetal Intestine Small	intestine
35	chr1:158968600-158970200	Active TSS	Fetal Thymus	thymus
36	chr1:158968600-158970200	Active TSS	Left Ventricle	heart
37	chr1:158968600-158970200	Active TSS	Placenta Amnion	Placenta Amnion
38	chr1:158968600-158970200	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr1:158968600-158970400	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr1:158968600-158970400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:158968600-158970400	Active TSS	Brain Hippocampus Middle	brain
42	chr1:158968600-158970400	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr1:158968600-158970600	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr1:158968600-158970600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr1:158968600-158970600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:158968600-158970600	Active TSS	Brain Cingulate Gyrus	brain
47	chr1:158968600-158970600	Active TSS	Fetal Intestine Large	intestine
48	chr1:158968600-158970600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
49	chr1:158968600-158970600	Active TSS	Fetal Stomach	stomach
50	chr1:158968600-158970600	Active TSS	Skeletal Muscle Male	skeletal muscle

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