Variant report

Variant	rs72960212
Chromosome Location	chr3:52720489-52720490
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:201)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:201 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr3:52719254-52720596	HepG2	liver:	n/a	n/a
2	EGR1	chr3:52719726-52720529	GM12878	blood:	n/a	chr3:52719978-52719987
3	MXI1	chr3:52717818-52721863	SK-N-SH	brain:	n/a	n/a
4	MYC	chr3:52719843-52720604	K562	blood:	n/a	n/a
5	MAX	chr3:52719369-52720661	K562	blood:	n/a	n/a
6	CREB1	chr3:52719248-52720777	HepG2	liver:	n/a	n/a
7	JUN	chr3:52719081-52720693	K562	blood:	n/a	chr3:52720134-52720143
8	POLR2A	chr3:52719217-52720995	Hela-S3	cervix:	n/a	n/a
9	MAX	chr3:52719846-52720518	HUVEC	blood vessel:	n/a	n/a
10	CREB1	chr3:52719310-52720525	GM12878	blood:	n/a	n/a
11	TBP	chr3:52718933-52720646	GM12878	blood:	n/a	n/a
12	MXI1	chr3:52719206-52722054	IMR90	lung:	n/a	n/a
13	POLR2A	chr3:52719219-52720858	HL-60	blood:	n/a	n/a
14	MAX	chr3:52719313-52720694	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:52719327-52720646	HCT-116	colon:	n/a	n/a
16	POLR2A	chr3:52718446-52723739	IMR90	lung:	n/a	n/a
17	MYC	chr3:52719709-52720594	MCF-7	breast:	n/a	n/a
18	STAT5A	chr3:52719267-52720912	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:52719241-52720951	U87	brain:	n/a	n/a
20	POLR2A	chr3:52719329-52721259	HepG2	liver:	n/a	n/a
21	POLR2A	chr3:52719170-52723469	H1-hESC	embryonic stem cell:	n/a	n/a
22	TAF1	chr3:52719268-52720508	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr3:52719314-52720507	MCF-7	breast:	n/a	n/a
24	POLR2A	chr3:52719130-52720824	U87	brain:	n/a	n/a
25	BHLHE40	chr3:52719302-52720749	GM12878	blood:	n/a	n/a
26	ELF1	chr3:52719277-52720552	GM12878	blood:	n/a	chr3:52720010-52720019
27	POLR2A	chr3:52718374-52724293	MCF10A-Er-Src	breast:	n/a	n/a
28	MYC	chr3:52719427-52720545	MCF-7	breast:	n/a	n/a
29	MTA3	chr3:52719726-52721101	GM12878	blood:	n/a	n/a
30	MXI1	chr3:52719313-52720573	HepG2	liver:	n/a	n/a
31	SIN3A	chr3:52719091-52721010	H1-hESC	embryonic stem cell:	n/a	chr3:52719716-52719729
32	BCLAF1	chr3:52719211-52720668	GM12878	blood:	n/a	chr3:52719712-52719725 chr3:52719935-52719948 chr3:52719439-52719448
33	MYC	chr3:52719815-52720535	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:52719330-52720633	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:52719328-52720571	GM19193	blood:	n/a	n/a
36	POLR2A	chr3:52719343-52721084	K562	blood:	n/a	n/a
37	SIN3AK20	chr3:52719298-52720643	MCF-7	breast:	n/a	n/a
38	MAX	chr3:52719386-52720559	K562	blood:	n/a	n/a
39	MYC	chr3:52719346-52720710	K562	blood:	n/a	n/a
40	MYC	chr3:52719795-52721134	MCF10A-Er-Src	breast:	n/a	n/a
41	MAX	chr3:52719391-52720628	Hela-S3	cervix:	n/a	n/a
42	SIN3AK20	chr3:52719302-52720549	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr3:52719322-52720556	MCF-7	breast:	n/a	n/a
44	POLR2A	chr3:52719342-52720593	ECC-1	luminal epithelium:	n/a	n/a
45	MAX	chr3:52719181-52720758	ECC-1	luminal epithelium:	n/a	n/a
46	HCFC1	chr3:52717761-52720928	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr3:52719302-52721063	HepG2	liver:	n/a	n/a
48	POLR2A	chr3:52719211-52720502	HUVEC	blood vessel:	n/a	n/a
49	NFIC	chr3:52719773-52720668	GM12878	blood:	n/a	n/a
50	RELA	chr3:52719310-52720555	GM19193	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52719561..52722875-chr3:52731308..52733675,5	MCF-7	breast:
2	chr15:49169692..49170233-chr3:52720055..52720663,2	NB4	blood:
3	chr3:52487997..52491865-chr3:52718755..52722667,5	MCF-7	breast:
4	chr12:7052820..7053734-chr3:52720037..52720875,2	Hela-S3	cervix:
5	chr3:52567553..52570571-chr3:52718365..52721514,3	MCF-7	breast:
6	chr3:52566406..52569677-chr3:52718507..52721358,5	MCF-7	breast:
7	chr3:52452815..52455679-chr3:52718724..52720785,2	MCF-7	breast:
8	chr3:52568115..52572187-chr3:52717267..52721555,8	K562	blood:
9	chr2:55646354..55647028-chr3:52720018..52720858,2	Hela-S3	cervix:
10	chr3:52567779..52572340-chr3:52718708..52722750,6	K562	blood:
11	chr3:52712073..52717938-chr3:52718038..52722104,14	K562	blood:
12	chr3:52492633..52495296-chr3:52719362..52721051,2	MCF-7	breast:
13	chr3:52718628..52724105-chr3:52738117..52743946,12	MCF-7	breast:
14	chr3:52718708..52722190-chr3:52722401..52727615,8	MCF-7	breast:
15	chr3:52719608..52722839-chr3:52830545..52833712,3	K562	blood:
16	chr3:52642339..52643982-chr3:52719145..52721917,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252787	TF binding region
PBRM1	TF binding region
GNL3	TF binding region
ENSG00000222345	TF binding region
SNORD19	TF binding region
SNORD19B	TF binding region
ENSG00000163938	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000162267	Chromatin interaction
ENSG00000255302	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000238923	Chromatin interaction
ENSG00000185634	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000252787	Chromatin interaction
ENSG00000111678	Chromatin interaction
ENSG00000016864	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000115355	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000238862	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000222345	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000212493	Chromatin interaction
ENSG00000212452	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11510435	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	1.00[EUR][1000 genomes]
rs17052357	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052404	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1963813	0.97[AFR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56134416	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56276589	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56665533	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57757646	1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58564212	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59638016	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59869286	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs61220667	1.00[EUR][1000 genomes]
rs61538294	1.00[EUR][1000 genomes]
rs6445536	1.00[EUR][1000 genomes]
rs6762788	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	0.87[EUR][1000 genomes]
rs6780397	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6803492	0.87[AFR][1000 genomes]
rs72947584	0.81[AFR][1000 genomes]
rs72950424	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960237	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960274	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960281	1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	1.00[EUR][1000 genomes]
rs72965181	1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52717800-52721000	Active TSS	GM12878-XiMat	blood
2	chr3:52718000-52720600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:52718000-52721200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:52718000-52721200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:52718200-52720600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:52718400-52720800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:52718400-52720800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:52718400-52720800	Active TSS	Fetal Thymus	thymus
9	chr3:52718400-52720800	Active TSS	NHLF	lung
10	chr3:52718400-52721200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:52718600-52720800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:52718600-52721200	Active TSS	Psoas Muscle	Psoas
13	chr3:52718800-52720600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:52718800-52720600	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:52718800-52720800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr3:52718800-52720800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:52718800-52720800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:52718800-52720800	Active TSS	Stomach Mucosa	stomach
19	chr3:52718800-52720800	Active TSS	HSMM	muscle
20	chr3:52718800-52720800	Active TSS	NHDF-Ad	bronchial
21	chr3:52718800-52721000	Active TSS	Right Atrium	heart
22	chr3:52718800-52721200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr3:52719000-52720600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:52719000-52720600	Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr3:52719000-52720600	Active TSS	Colon Smooth Muscle	Colon
26	chr3:52719000-52720600	Active TSS	Fetal Heart	heart
27	chr3:52719000-52720600	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr3:52719000-52720600	Active TSS	A549	lung
29	chr3:52719000-52720800	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr3:52719000-52720800	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr3:52719000-52720800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:52719000-52720800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:52719000-52720800	Active TSS	Fetal Kidney	kidney
34	chr3:52719000-52720800	Active TSS	Fetal Lung	lung
35	chr3:52719000-52720800	Active TSS	Fetal Muscle Trunk	muscle
36	chr3:52719000-52720800	Active TSS	Fetal Muscle Leg	muscle
37	chr3:52719000-52720800	Active TSS	Placenta	Placenta
38	chr3:52719000-52720800	Active TSS	Fetal Stomach	stomach
39	chr3:52719000-52720800	Active TSS	Hela-S3	cervix
40	chr3:52719000-52720800	Active TSS	HMEC	breast
41	chr3:52719000-52720800	Active TSS	HSMMtube	muscle
42	chr3:52719000-52720800	Active TSS	HUVEC	blood vessel
43	chr3:52719000-52720800	Active TSS	NH-A	brain
44	chr3:52719000-52720800	Active TSS	Osteobl	bone
45	chr3:52719000-52721000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:52719000-52721000	Active TSS	Fetal Intestine Large	intestine
47	chr3:52719000-52721400	Active TSS	Colonic Mucosa	Colon
48	chr3:52719200-52720800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:52719200-52720800	Active TSS	H9 Cell Line	embryonic stem cell
50	chr3:52719200-52720800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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