Variant report

Variant	rs72960288
Chromosome Location	chr3:52809509-52809510
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	HEY1	chr3:52809155-52810388	HepG2	liver:	n/a	n/a
2	MAZ	chr3:52809409-52810100	HepG2	liver:	n/a	chr3:52809645-52809655
3	EP300	chr3:52809222-52809864	HepG2	liver:	n/a	n/a
4	JUND	chr3:52809353-52809671	HepG2	liver:	n/a	n/a
5	MYBL2	chr3:52809212-52809898	HepG2	liver:	n/a	n/a
6	EP300	chr3:52809362-52809794	HepG2	liver:	n/a	n/a
7	RXRA	chr3:52809240-52809948	HepG2	liver:	n/a	chr3:52809546-52809568 chr3:52809547-52809566
8	BHLHE40	chr3:52809404-52809990	HepG2	liver:	n/a	n/a
9	HDAC2	chr3:52809333-52809932	HepG2	liver:	n/a	chr3:52809604-52809612
10	JUND	chr3:52809487-52809720	HepG2	liver:	n/a	n/a
11	NR2F2	chr3:52809203-52809986	HepG2	liver:	n/a	n/a
12	RCOR1	chr3:52809322-52810142	HepG2	liver:	n/a	n/a
13	HNF4G	chr3:52809294-52809824	HepG2	liver:	n/a	chr3:52809617-52809625 chr3:52809599-52809611 chr3:52809599-52809611 chr3:52809604-52809612
14	JUND	chr3:52809346-52809784	HepG2	liver:	n/a	n/a
15	TEAD4	chr3:52809235-52809975	HepG2	liver:	n/a	n/a
16	HEY1	chr3:52809257-52809858	HepG2	liver:	n/a	n/a
17	MYBL2	chr3:52808979-52810238	HepG2	liver:	n/a	n/a
18	FOXA1	chr3:52809202-52809891	HepG2	liver:	n/a	n/a
19	MAFF	chr3:52809302-52809663	HepG2	liver:	n/a	n/a
20	HDAC2	chr3:52809241-52809854	HepG2	liver:	n/a	chr3:52809604-52809612
21	ZBTB7A	chr3:52809442-52809758	HepG2	liver:	n/a	n/a
22	CEBPD	chr3:52809290-52809838	HepG2	liver:	n/a	n/a
23	EP300	chr3:52809215-52809880	HepG2	liver:	n/a	n/a
24	MAFK	chr3:52809327-52809765	HepG2	liver:	n/a	n/a
25	POLR2A	chr3:52809204-52810353	HepG2	liver:	n/a	n/a
26	NFIC	chr3:52809062-52809890	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:52809258-52809843	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:52809274-52809789	HepG2	liver:	n/a	n/a
29	FOXA1	chr3:52809320-52809840	HepG2	liver:	n/a	n/a
30	ZBTB7A	chr3:52809509-52809811	HepG2	liver:	n/a	n/a
31	FOXA1	chr3:52809219-52809909	HepG2	liver:	n/a	n/a
32	HNF4A	chr3:52809331-52809836	HepG2	liver:	n/a	chr3:52809617-52809625 chr3:52809599-52809611 chr3:52809599-52809611 chr3:52809604-52809612 chr3:52809597-52809612
33	POLR2A	chr3:52809398-52809996	HepG2	liver:	n/a	n/a
34	ARID3A	chr3:52809312-52809832	HepG2	liver:	n/a	n/a
35	REST	chr3:52809312-52809851	HepG2	liver:	n/a	n/a
36	CHD2	chr3:52809433-52809710	HepG2	liver:	n/a	n/a
37	RAD21	chr3:52809335-52809726	HepG2	liver:	n/a	n/a
38	RAD21	chr3:52809328-52809813	HepG2	liver:	n/a	n/a
39	RXRA	chr3:52809302-52809848	HepG2	liver:	n/a	chr3:52809546-52809568 chr3:52809547-52809566
40	FOXA1	chr3:52808650-52809785	HepG2	liver:	n/a	n/a
41	FOSL2	chr3:52809247-52809762	HepG2	liver:	n/a	n/a
42	TCF12	chr3:52809298-52809738	HepG2	liver:	n/a	chr3:52809423-52809431
43	HNF4A	chr3:52809278-52809804	HepG2	liver:	n/a	chr3:52809617-52809625 chr3:52809599-52809611 chr3:52809599-52809611 chr3:52809604-52809612 chr3:52809597-52809612
44	MBD4	chr3:52809216-52809863	HepG2	liver:	n/a	n/a
45	SMC3	chr3:52809327-52810020	HepG2	liver:	n/a	n/a
46	TCF7L2	chr3:52809310-52809794	HepG2	liver:	n/a	n/a
47	MXI1	chr3:52809301-52809749	HepG2	liver:	n/a	n/a
48	NFIC	chr3:52809153-52810071	HepG2	liver:	n/a	n/a
49	SP1	chr3:52809190-52809936	HepG2	liver:	n/a	n/a
50	HNF4G	chr3:52809307-52809932	HepG2	liver:	n/a	chr3:52809617-52809625 chr3:52809599-52809611 chr3:52809599-52809611 chr3:52809604-52809612

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52799929..52802463-chr3:52808466..52811160,2	K562	blood:

Variant related genes	Relation type
NEK4	TF binding region
ITIH1	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17052424	0.82[AFR][1000 genomes]
rs57787182	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59227741	1.00[AMR][1000 genomes]
rs72954371	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72960294	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
2	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1010761	chr3:52804547-52851258	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52805400-52809600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:52805600-52809600	Weak transcription	Thymus	Thymus
3	chr3:52805600-52825800	Weak transcription	Right Ventricle	heart
4	chr3:52805800-52810000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:52805800-52812000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:52806000-52810000	Weak transcription	Pancreas	Pancrea
7	chr3:52806000-52811600	Weak transcription	Adipose Nuclei	Adipose
8	chr3:52806800-52810400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:52808600-52810800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:52808600-52811200	Enhancers	Fetal Intestine Large	intestine
11	chr3:52808600-52812000	Enhancers	Fetal Intestine Small	intestine
12	chr3:52808800-52810200	Flanking Active TSS	HepG2	liver
13	chr3:52808800-52810600	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr3:52809000-52810200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:52809000-52811400	Enhancers	Stomach Mucosa	stomach
16	chr3:52809200-52810000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:52809200-52810200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr3:52809200-52810200	Enhancers	Fetal Heart	heart
19	chr3:52809200-52810800	Enhancers	Fetal Thymus	thymus
20	chr3:52809400-52809800	Enhancers	Liver	Liver
21	chr3:52809400-52810400	Enhancers	K562	blood

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