Variant report

Variant	rs2286797
Chromosome Location	chr3:52829633-52829634
allele	C/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	MAFK	chr3:52829463-52829635	HepG2	liver:	n/a	n/a
2	JUND	chr3:52829410-52829701	HepG2	liver:	n/a	chr3:52829505-52829514
3	TEAD4	chr3:52829312-52829741	HepG2	liver:	n/a	n/a
4	YY1	chr3:52829402-52829913	HepG2	liver:	n/a	chr3:52829507-52829518
5	MYBL2	chr3:52829323-52829846	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:52829400-52829859	HepG2	liver:	n/a	n/a
7	SIN3AK20	chr3:52829499-52829797	HepG2	liver:	n/a	n/a
8	REST	chr3:52829319-52829774	HepG2	liver:	n/a	n/a
9	MBD4	chr3:52829310-52829780	HepG2	liver:	n/a	n/a
10	FOXA1	chr3:52829295-52829857	HepG2	liver:	n/a	chr3:52829595-52829607
11	FOXA1	chr3:52829364-52829855	HepG2	liver:	n/a	chr3:52829595-52829607
12	MAX	chr3:52829176-52829949	HepG2	liver:	n/a	chr3:52829250-52829260
13	FOSL2	chr3:52829354-52829862	HepG2	liver:	n/a	chr3:52829505-52829514
14	MBD4	chr3:52828999-52829868	HepG2	liver:	n/a	n/a
15	MXI1	chr3:52829366-52829819	HepG2	liver:	n/a	n/a
16	MYBL2	chr3:52829213-52829890	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:52828113-52829875	HepG2	liver:	n/a	n/a
18	FOXA2	chr3:52829466-52829715	HepG2	liver:	n/a	chr3:52829595-52829607
19	HEY1	chr3:52829202-52829927	HepG2	liver:	n/a	chr3:52829253-52829268
20	TCF12	chr3:52829374-52829769	HepG2	liver:	n/a	n/a
21	NFIC	chr3:52829117-52829872	HepG2	liver:	n/a	n/a
22	SP1	chr3:52829310-52829909	HepG2	liver:	n/a	chr3:52829502-52829516
23	POLR2A	chr3:52829624-52829888	HepG2	liver:	n/a	n/a
24	HNF4A	chr3:52829417-52829748	HepG2	liver:	n/a	n/a
25	SIN3AK20	chr3:52829478-52829824	HepG2	liver:	n/a	n/a
26	MAZ	chr3:52829306-52829693	HepG2	liver:	n/a	n/a
27	EP300	chr3:52829390-52829839	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:52829295-52829888	HepG2	liver:	n/a	n/a
29	EP300	chr3:52829262-52829875	HepG2	liver:	n/a	n/a
30	MAX	chr3:52828001-52830006	HepG2	liver:	n/a	chr3:52829250-52829260
31	FOXA1	chr3:52829347-52829878	HepG2	liver:	n/a	chr3:52829595-52829607
32	ELF1	chr3:52829457-52829764	HepG2	liver:	n/a	n/a
33	FOXA1	chr3:52829343-52829807	HepG2	liver:	n/a	chr3:52829595-52829607
34	MAX	chr3:52829491-52829691	HepG2	liver:	n/a	n/a
35	RXRA	chr3:52829354-52829812	HepG2	liver:	n/a	n/a
36	MYC	chr3:52829431-52829783	HepG2	liver:	n/a	n/a
37	CEBPD	chr3:52829391-52829764	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52802780..52807602-chr3:52827391..52831755,5	K562	blood:
2	chr3:52804000..52806287-chr3:52829373..52831627,2	MCF-7	breast:
3	chr3:52827101..52830669-chr3:52833208..52834941,3	K562	blood:
4	chr3:52812843..52815732-chr3:52828403..52831078,2	K562	blood:
5	chr3:52828891..52830949-chr3:52832398..52834314,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ITIH3-2	chr3:52829619-52830057	NONHSAT089957

Variant related genes	Relation type
ITIH3	TF binding region
ENSG00000162267	Chromatin interaction
ENSG00000055957	Chromatin interaction
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2286799	1.00[EUR][1000 genomes]
rs3733042	1.00[EUR][1000 genomes]
rs3774356	0.84[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3774362	0.80[AMR][1000 genomes]
rs4629327	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52824000-52832800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52825800-52836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:52827000-52830600	Enhancers	Spleen	Spleen
4	chr3:52827600-52829800	Flanking Active TSS	HepG2	liver
5	chr3:52827800-52830000	Enhancers	Fetal Muscle Trunk	muscle
6	chr3:52827800-52832000	Weak transcription	HSMM	muscle
7	chr3:52828000-52830200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:52828200-52835800	Weak transcription	HSMMtube	muscle
9	chr3:52828600-52832600	Weak transcription	Stomach Mucosa	stomach
10	chr3:52828800-52830400	Enhancers	Pancreas	Pancrea
11	chr3:52829000-52829800	Active TSS	Liver	Liver
12	chr3:52829000-52830000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:52829000-52830400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:52829000-52832200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:52829000-52832400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:52829000-52834200	Weak transcription	Brain Substantia Nigra	brain
17	chr3:52829200-52830200	Enhancers	Fetal Thymus	thymus
18	chr3:52829600-52830000	Enhancers	Primary hematopoietic stem cells	blood
19	chr3:52829600-52832400	Weak transcription	Placenta	Placenta

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