Variant report

Variant	rs12060663
Chromosome Location	chr1:57111833-57111834
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	TBP	chr1:57110901-57111920	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:57110683-57111977	H1-hESC	embryonic stem cell:	n/a	n/a
3	KAP1	chr1:57111524-57112038	U2OS	brain:	n/a	n/a
4	CHD1	chr1:57111728-57111940	H1-hESC	embryonic stem cell:	n/a	n/a
5	RCOR1	chr1:57110073-57112051	Hela-S3	cervix:	n/a	n/a
6	TEAD4	chr1:57110919-57112036	ECC-1	luminal epithelium:	n/a	n/a
7	MAZ	chr1:57109756-57111909	IMR90	lung:	n/a	n/a
8	ZNF263	chr1:57110992-57112084	HEK293-T-REx	kidney:	n/a	n/a
9	TEAD4	chr1:57111660-57111979	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:57111269-57111880	Hela-S3	cervix:	n/a	n/a
11	TBP	chr1:57111495-57112171	Hela-S3	cervix:	n/a	n/a
12	TEAD4	chr1:57111577-57112168	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:57110442-57111954	H1-hESC	embryonic stem cell:	n/a	n/a
14	SMARCB1	chr1:57109860-57111913	Hela-S3	cervix:	n/a	n/a
15	E2F4	chr1:57111781-57112084	MCF10A-Er-Src	breast:	n/a	n/a
16	SMC3	chr1:57111370-57112061	Hela-S3	cervix:	n/a	n/a
17	TAF1	chr1:57110896-57111956	H1-hESC	embryonic stem cell:	n/a	n/a
18	GTF2F1	chr1:57111414-57112145	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:57111344-57111880	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:57110267-57111969	Hela-S3	cervix:	n/a	n/a
21	YY1	chr1:57111544-57111936	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:57110068-57112007	Hela-S3	cervix:	n/a	n/a
23	MXI1	chr1:57111051-57112023	Hela-S3	cervix:	n/a	n/a
24	SIN3A	chr1:57110934-57112065	H1-hESC	embryonic stem cell:	n/a	chr1:57111263-57111276
25	POLR2A	chr1:57110276-57111893	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:57109759-57112147	Hela-S3	cervix:	n/a	n/a
27	YY1	chr1:57111481-57112032	H1-hESC	embryonic stem cell:	n/a	n/a
28	REST	chr1:57110268-57112005	H1-neurons	neurons:	n/a	chr1:57110757-57110767 chr1:57110821-57110831 chr1:57110714-57110732 chr1:57110975-57110988 chr1:57110779-57110797 chr1:57111028-57111041 chr1:57111263-57111276
29	MAZ	chr1:57110319-57111885	Hela-S3	cervix:	n/a	n/a
30	MAX	chr1:57110040-57111965	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PPAP2B	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10437072	0.92[AFR][1000 genomes]
rs11206874	1.00[AMR][1000 genomes]
rs11206876	1.00[AMR][1000 genomes]
rs11206904	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12076595	0.92[AFR][1000 genomes]
rs12081693	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12086954	0.92[AFR][1000 genomes]
rs12089982	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12090117	1.00[AMR][1000 genomes]
rs12094381	1.00[AMR][1000 genomes]
rs12095026	1.00[AMR][1000 genomes]
rs13376460	1.00[AMR][1000 genomes]
rs2897036	1.00[AMR][1000 genomes]
rs3991779	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3371942	chr1:57109389-57112237	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3402388	chr1:57109989-57112537	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3445991	chr1:57110114-57112162	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57109800-57112000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:57109800-57112000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:57109800-57112000	Active TSS	Psoas Muscle	Psoas
4	chr1:57109800-57112200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:57109800-57112200	Active TSS	Brain Angular Gyrus	brain
6	chr1:57109800-57112400	Active TSS	Rectal Smooth Muscle	rectum
7	chr1:57109800-57113200	Active TSS	Right Atrium	heart
8	chr1:57109800-57114600	Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr1:57110000-57112000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr1:57110000-57112000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:57110000-57112000	Active TSS	Fetal Brain Female	brain
12	chr1:57110000-57112000	Bivalent/Poised TSS	Osteobl	bone
13	chr1:57110000-57112200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:57110000-57112200	Active TSS	Brain Cingulate Gyrus	brain
15	chr1:57110000-57112200	Active TSS	Hela-S3	cervix
16	chr1:57110000-57112400	Active TSS	Brain Anterior Caudate	brain
17	chr1:57110000-57112400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:57110000-57112400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:57110000-57112600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:57110000-57113200	Active TSS	Stomach Smooth Muscle	stomach
21	chr1:57110000-57113400	Active TSS	Right Ventricle	heart
22	chr1:57110200-57112000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:57110200-57112000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr1:57110200-57112000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:57110200-57112000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:57110200-57112200	Active TSS	Aorta	Aorta
27	chr1:57110200-57112600	Active TSS	Left Ventricle	heart
28	chr1:57110200-57112600	Active TSS	A549	lung
29	chr1:57110200-57113000	Active TSS	Fetal Heart	heart
30	chr1:57110400-57112000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:57110400-57112000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:57110400-57112000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:57110400-57112000	Active TSS	Esophagus	oesophagus
34	chr1:57110400-57112600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr1:57110600-57112000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:57110600-57112400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
37	chr1:57111000-57112000	Bivalent/Poised TSS	Colonic Mucosa	Colon
38	chr1:57111200-57112000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr1:57111400-57112000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:57111400-57112000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:57111400-57112000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:57111400-57112000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:57111400-57112000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:57111400-57112000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:57111400-57112000	Flanking Active TSS	Liver	Liver
46	chr1:57111400-57112000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
47	chr1:57111400-57112000	Bivalent/Poised TSS	HepG2	liver
48	chr1:57111400-57112200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:57111400-57112200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:57111400-57112200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum

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