Variant report

Variant	rs12079723
Chromosome Location	chr1:94147019-94147020
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	CCNT2	chr1:94146686-94147550	K562	blood:	n/a	chr1:94146948-94146957 chr1:94146969-94146978
2	SIN3AK20	chr1:94146942-94147549	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr1:94144711-94147850	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr1:94145966-94147845	GM18505	blood:	n/a	n/a
5	TAF1	chr1:94146220-94147761	SK-N-SH	brain:	n/a	n/a
6	ZBTB7A	chr1:94146594-94147264	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr1:94145972-94147860	A549	lung:	n/a	n/a
8	SIN3A	chr1:94146116-94147796	H1-hESC	embryonic stem cell:	n/a	chr1:94146813-94146826 chr1:94146820-94146829 chr1:94147370-94147381 chr1:94147368-94147381
9	GATA3	chr1:94144424-94147772	SK-N-SH	brain:	n/a	chr1:94144834-94144846 chr1:94144821-94144828 chr1:94145364-94145374 chr1:94144837-94144844 chr1:94144835-94144845 chr1:94145364-94145373 chr1:94147594-94147604 chr1:94144817-94144833 chr1:94144837-94144844 chr1:94144821-94144828 chr1:94144817-94144833 chr1:94145122-94145131 chr1:94144821-94144828 chr1:94145019-94145027 chr1:94144837-94144844
10	MAZ	chr1:94145815-94147841	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:94145711-94147828	Hela-S3	cervix:	n/a	n/a
12	HA-E2F1	chr1:94146826-94147574	Hela-S3	cervix:	n/a	chr1:94147096-94147106 chr1:94146969-94146978 chr1:94147399-94147408
13	POLR2A	chr1:94146207-94147768	HUVEC	blood vessel:	n/a	n/a
14	MAX	chr1:94145818-94147792	Hela-S3	cervix:	n/a	n/a
15	CREB1	chr1:94147017-94147593	A549	lung:	n/a	n/a
16	TCF12	chr1:94146940-94147744	ECC-1	luminal epithelium:	n/a	chr1:94147700-94147707
17	SMARCC1	chr1:94145728-94147882	Hela-S3	cervix:	n/a	n/a
18	MAZ	chr1:94146986-94147567	K562	blood:	n/a	n/a
19	POLR2A	chr1:94146913-94147858	SK-N-SH	brain:	n/a	n/a
20	TCF7L2	chr1:94146835-94147536	HCT-116	colon:	n/a	n/a
21	POLR2A	chr1:94146956-94147765	MCF10A-Er-Src	breast:	n/a	n/a
22	CTBP2	chr1:94146302-94147682	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr1:94146851-94147709	Gliobla	brain:	n/a	n/a
24	POLR2A	chr1:94146807-94147792	GM12892	blood:	n/a	n/a
25	SMC3	chr1:94144843-94148119	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:94145532-94148138	HUVEC	blood vessel:	n/a	n/a
27	POLR2A	chr1:94146932-94147683	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr1:94146279-94147760	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr1:94145562-94147935	Hela-S3	cervix:	n/a	n/a
30	CHD2	chr1:94145768-94147834	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr1:94145540-94147852	HUVEC	blood vessel:	n/a	n/a
32	CTCF	chr1:94147000-94147150	GM12873	blood:	n/a	n/a
33	POLR2A	chr1:94147005-94147686	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTCF	chr1:94145771-94147942	SK-N-SH	brain:	n/a	chr1:94147374-94147387 chr1:94147374-94147387 chr1:94147846-94147854
35	SMARCB1	chr1:94145811-94147889	Hela-S3	cervix:	n/a	n/a
36	USF2	chr1:94146928-94147166	Hela-S3	cervix:	n/a	chr1:94146989-94147005
37	POLR2A	chr1:94146209-94147625	A549	lung:	n/a	n/a
38	POLR2A	chr1:94146751-94147642	A549	lung:	n/a	n/a
39	POLR2A	chr1:94146859-94147568	MCF-7	breast:	n/a	n/a
40	POLR2A	chr1:94146290-94147815	GM15510	blood:	n/a	n/a
41	RCOR1	chr1:94147010-94147847	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr1:94146996-94148138	A549	lung:	n/a	chr1:94147374-94147387 chr1:94147374-94147387 chr1:94147846-94147854
43	SMC3	chr1:94145677-94147902	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr1:94145689-94147921	IMR90	lung:	n/a	n/a
45	POLR2A	chr1:94145466-94147905	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr1:94147015-94147626	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr1:94146171-94147857	ProgFib	skin:	n/a	n/a
48	RAD21	chr1:94145132-94148255	SK-N-SH	brain:	n/a	chr1:94147371-94147385 chr1:94147373-94147387
49	POLR2A	chr1:94146997-94147757	HCT-116	colon:	n/a	n/a
50	MAZ	chr1:94145632-94148061	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:94146697..94147495-chr11:68038998..68039926,2	Hela-S3	cervix:
2	chr1:94146477..94147235-chr19:36605467..36606382,2	Hela-S3	cervix:
3	chr1:94146501..94148043-chr1:94311466..94313377,2	MCF-7	breast:
4	chr1:94146452..94147094-chr5:79551449..79552398,2	Hela-S3	cervix:
5	chr1:94146402..94147127-chr6:133135595..133136405,2	Hela-S3	cervix:
6	chr1:94144888..94147261-chr1:94311172..94313468,2	K562	blood:
7	chr1:93913059..93915471-chr1:94146480..94149352,2	MCF-7	breast:
8	chr1:94145898..94148493-chr1:94311257..94313086,3	MCF-7	breast:

Variant related genes	Relation type
BCAR3	TF binding region
ENSG00000211575	Chromatin interaction
ENSG00000171067	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000112306	Chromatin interaction
ENSG00000137936	Chromatin interaction
ENSG00000105258	Chromatin interaction
ENSG00000164300	Chromatin interaction
ENSG00000105254	Chromatin interaction
ENSG00000137942	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1011903	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011904	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164961	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164962	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164963	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057736	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12059154	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12084853	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12092517	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1567791	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61781002	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541386	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541387	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6541388	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6541389	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6656270	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6657709	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6660740	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6675484	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6684568	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6694536	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6701871	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6702036	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6704479	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7519952	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs955470	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9659100	0.83[EUR][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	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
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94144400-94148200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:94144600-94148400	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr1:94145000-94148000	Active TSS	Brain Anterior Caudate	brain
4	chr1:94145200-94148000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:94145400-94147600	Active TSS	Muscle Satellite Cultured Cells	--
6	chr1:94145400-94147800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:94145400-94148400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:94145400-94148400	Active TSS	HSMM	muscle
9	chr1:94145600-94147600	Active TSS	Fetal Kidney	kidney
10	chr1:94145600-94147800	Active TSS	NHDF-Ad	bronchial
11	chr1:94145600-94148000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:94145600-94148200	Active TSS	A549	lung
13	chr1:94145800-94147400	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr1:94145800-94147600	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:94145800-94147600	Active TSS	Hela-S3	cervix
16	chr1:94145800-94148000	Active TSS	H9 Cell Line	embryonic stem cell
17	chr1:94145800-94148000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:94145800-94148000	Bivalent/Poised TSS	Fetal Brain Female	brain
19	chr1:94145800-94148000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr1:94145800-94148200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr1:94146000-94147200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
22	chr1:94146000-94147600	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:94146000-94147600	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr1:94146000-94147800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr1:94146000-94147800	Active TSS	Ovary	ovary
26	chr1:94146000-94148000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:94146000-94148200	Active TSS	Brain Angular Gyrus	brain
28	chr1:94146200-94147200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr1:94146200-94147200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:94146200-94147200	Bivalent Enhancer	Fetal Heart	heart
31	chr1:94146200-94147400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:94146200-94147400	Active TSS	Esophagus	oesophagus
33	chr1:94146200-94147400	Bivalent/Poised TSS	Fetal Stomach	stomach
34	chr1:94146200-94147400	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr1:94146200-94147600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:94146200-94147600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:94146200-94147600	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr1:94146200-94147600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:94146200-94147600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr1:94146200-94147600	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr1:94146200-94147600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:94146200-94147600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:94146200-94147600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:94146200-94147600	Active TSS	Colon Smooth Muscle	Colon
45	chr1:94146200-94147600	Active TSS	Duodenum Mucosa	Duodenum
46	chr1:94146200-94147600	Active TSS	Placenta	Placenta
47	chr1:94146200-94147600	Active TSS	Lung	lung
48	chr1:94146200-94147800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:94146200-94147800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:94146200-94147800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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