Variant report

Variant	rs28365912
Chromosome Location	chr1:57045587-57045588
allele	A/C/G/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	RAD21	chr1:57044639-57045623	Hela-S3	cervix:	n/a	n/a
2	SMC3	chr1:57042431-57046218	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr1:57045440-57045590	HFF-Myc	foreskin:	n/a	n/a
4	MAZ	chr1:57043020-57045658	IMR90	lung:	n/a	chr1:57045272-57045281 chr1:57044379-57044389
5	CTCF	chr1:57045130-57045619	K562	blood:	n/a	n/a
6	RAD21	chr1:57045081-57045709	A549	lung:	n/a	n/a
7	NRF1	chr1:57043965-57045691	SK-N-SH	brain:	n/a	n/a
8	RAD21	chr1:57044882-57045631	MCF-7	breast:	n/a	n/a
9	CTCF	chr1:57045259-57045593	A549	lung:	n/a	n/a
10	CTCF	chr1:57045055-57045655	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:57044583-57045711	PFSK-1	brain:	n/a	n/a
12	FOXA1	chr1:57045293-57045844	HepG2	liver:	n/a	chr1:57045667-57045679
13	ZNF263	chr1:57042620-57045777	HEK293-T-REx	kidney:	n/a	chr1:57045140-57045161
14	RAD21	chr1:57044844-57045642	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr1:57045270-57045610	K562	blood:	n/a	n/a
16	ZNF143	chr1:57045015-57045602	H1-hESC	embryonic stem cell:	n/a	n/a
17	TEAD4	chr1:57044754-57045612	SK-N-SH	brain:	n/a	n/a
18	RAD21	chr1:57044826-57045690	HCT-116	colon:	n/a	n/a
19	E2F4	chr1:57044872-57045911	MCF10A-Er-Src	breast:	n/a	n/a
20	MXI1	chr1:57042534-57045906	IMR90	lung:	n/a	n/a
21	PRDM1	chr1:57045064-57045641	Hela-S3	cervix:	n/a	chr1:57045418-57045432 chr1:57045417-57045432
22	CTCF	chr1:57045380-57045670	HL-60	blood:	n/a	n/a
23	ZNF143	chr1:57044988-57045634	GM12878	blood:	n/a	n/a
24	RAD21	chr1:57044837-57045755	HepG2	liver:	n/a	n/a
25	CTCF	chr1:57044847-57045810	A549	lung:	n/a	n/a
26	CTCF	chr1:57044956-57045719	IMR90	lung:	n/a	n/a
27	CTCF	chr1:57044899-57045764	HCT-116	colon:	n/a	n/a
28	RAD21	chr1:57042027-57046443	SK-N-SH	brain:	n/a	n/a
29	RAD21	chr1:57044890-57045690	A549	lung:	n/a	n/a
30	CTCF	chr1:57045440-57045590	GM06990	blood:	n/a	n/a
31	MAFK	chr1:57044913-57045604	Hela-S3	cervix:	n/a	n/a
32	ZNF384	chr1:57045147-57045618	K562	blood:	n/a	n/a
33	RAD21	chr1:57042764-57045668	IMR90	lung:	n/a	n/a
34	ZNF384	chr1:57044867-57045727	GM12878	blood:	n/a	n/a
35	STAT1	chr1:57045373-57045892	GM12878	blood:	n/a	n/a
36	EP300	chr1:57044441-57045697	SK-N-SH	brain:	n/a	chr1:57045398-57045412 chr1:57044807-57044823 chr1:57045399-57045413
37	TCF12	chr1:57044587-57045664	SK-N-SH	brain:	n/a	n/a
38	RAD21	chr1:57044824-57045611	HepG2	liver:	n/a	n/a
39	SMC3	chr1:57045060-57045625	HepG2	liver:	n/a	n/a
40	RAD21	chr1:57044779-57045712	HCT-116	colon:	n/a	n/a
41	RAD21	chr1:57044531-57045639	SK-N-SH_RA	brain:	n/a	n/a
42	ARID3A	chr1:57044884-57045733	HepG2	liver:	n/a	n/a
43	SIN3AK20	chr1:57044821-57045611	SK-N-SH	brain:	n/a	n/a
44	PBX3	chr1:57044908-57045590	SK-N-SH	brain:	n/a	n/a
45	RAD21	chr1:57043764-57045657	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr1:57045440-57045590	HMEC	breast:	n/a	n/a
47	RAD21	chr1:57044910-57045625	SK-N-SH_RA	brain:	n/a	n/a
48	NFIC	chr1:57044722-57045651	SK-N-SH	brain:	n/a	n/a
49	RAD21	chr1:57044867-57045636	H1-hESC	embryonic stem cell:	n/a	n/a
50	BRCA1	chr1:57044840-57045720	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
PPAP2B	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11206845	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12058459	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12058536	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12059747	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12059843	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12070247	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12070557	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12090895	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12098117	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17114119	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17114125	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1953114	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6687908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6702052	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72903425	1.00[EUR][1000 genomes];0.94[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	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

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57039600-57046000	Active TSS	Right Atrium	heart
2	chr1:57040000-57045600	Active TSS	Brain Angular Gyrus	brain
3	chr1:57040000-57046000	Active TSS	Ovary	ovary
4	chr1:57040200-57045800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:57040200-57046000	Active TSS	Right Ventricle	heart
6	chr1:57040400-57045600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr1:57040600-57045600	Active TSS	Brain Cingulate Gyrus	brain
8	chr1:57040800-57045600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:57040800-57045800	Active TSS	Placenta Amnion	Placenta Amnion
10	chr1:57041000-57045600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr1:57041000-57045800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr1:57041200-57045600	Active TSS	Muscle Satellite Cultured Cells	--
13	chr1:57041200-57045600	Active TSS	Aorta	Aorta
14	chr1:57041400-57045600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:57041400-57045600	Active TSS	Liver	Liver
16	chr1:57041800-57045600	Active TSS	Brain Hippocampus Middle	brain
17	chr1:57041800-57046000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:57042000-57045600	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:57042000-57045600	Active TSS	Fetal Intestine Large	intestine
20	chr1:57042000-57045800	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr1:57042200-57045800	Active TSS	Left Ventricle	heart
22	chr1:57042400-57045800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:57042400-57045800	Active TSS	Colonic Mucosa	Colon
24	chr1:57042400-57045800	Active TSS	Fetal Intestine Small	intestine
25	chr1:57042400-57045800	Active TSS	HSMMtube	muscle
26	chr1:57042600-57045600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:57042600-57045600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:57042600-57045600	Active TSS	HSMM	muscle
29	chr1:57042800-57045600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr1:57042800-57045600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr1:57042800-57045600	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr1:57042800-57045800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:57042800-57045800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:57043000-57045600	Active TSS	Fetal Kidney	kidney
35	chr1:57043000-57045600	Active TSS	Psoas Muscle	Psoas
36	chr1:57043000-57046000	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr1:57043200-57045600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:57043200-57045600	Active TSS	Osteobl	bone
39	chr1:57043400-57045600	Active TSS	NHDF-Ad	bronchial
40	chr1:57043400-57045800	Active TSS	Colon Smooth Muscle	Colon
41	chr1:57043400-57046000	Active TSS	Thymus	Thymus
42	chr1:57043600-57045600	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr1:57043600-57045600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:57043600-57045600	Active TSS	Fetal Muscle Leg	muscle
45	chr1:57043600-57045600	Active TSS	Placenta	Placenta
46	chr1:57043600-57045600	Active TSS	Fetal Stomach	stomach
47	chr1:57043600-57045600	Active TSS	A549	lung
48	chr1:57043600-57045600	Active TSS	NHEK	skin
49	chr1:57043800-57045600	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr1:57043800-57045600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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