Variant report

Variant	rs2293025
Chromosome Location	chr3:46620760-46620761
allele	A/C
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	NANOG	chr3:46620505-46620800	H1-hESC	embryonic stem cell:	n/a	chr3:46620544-46620558
2	SPI1	chr3:46620382-46620789	HL-60	blood:	n/a	chr3:46620569-46620582 chr3:46620568-46620581 chr3:46620571-46620578 chr3:46620570-46620579
3	FOXA1	chr3:46620329-46620795	HepG2	liver:	n/a	n/a
4	MBD4	chr3:46620342-46620813	HepG2	liver:	n/a	n/a
5	ELF1	chr3:46620427-46620795	HepG2	liver:	n/a	chr3:46620570-46620581
6	TCF7L2	chr3:46620294-46621228	HepG2	liver:	n/a	chr3:46620308-46620322
7	FOXA1	chr3:46620418-46620800	HepG2	liver:	n/a	n/a
8	MAX	chr3:46620564-46620901	H1-hESC	embryonic stem cell:	n/a	n/a
9	NFIC	chr3:46620392-46620821	HepG2	liver:	n/a	n/a
10	TCF7L2	chr3:46620443-46620887	HCT-116	colon:	n/a	n/a
11	MAX	chr3:46620309-46621152	HepG2	liver:	n/a	n/a
12	SP1	chr3:46620393-46620853	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:46620748-46621730	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOXA2	chr3:46620373-46620776	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr3:46620487-46620980	H1-hESC	embryonic stem cell:	n/a	n/a
16	EP300	chr3:46620267-46620855	HepG2	liver:	n/a	chr3:46620570-46620579 chr3:46620566-46620580
17	POLR2A	chr3:46620710-46620940	H1-hESC	embryonic stem cell:	n/a	n/a
18	EP300	chr3:46620363-46620875	HepG2	liver:	n/a	chr3:46620570-46620579 chr3:46620566-46620580
19	NFIC	chr3:46620261-46620890	HepG2	liver:	n/a	n/a
20	SIN3A	chr3:46620390-46621386	H1-hESC	embryonic stem cell:	n/a	n/a
21	HDAC2	chr3:46620341-46620811	HepG2	liver:	n/a	n/a
22	POLR2A	chr3:46620740-46620948	H1-hESC	embryonic stem cell:	n/a	n/a
23	RXRA	chr3:46620438-46620770	HepG2	liver:	n/a	chr3:46620572-46620581
24	SPI1	chr3:46620476-46620777	HL-60	blood:	n/a	chr3:46620569-46620582 chr3:46620568-46620581 chr3:46620571-46620578 chr3:46620570-46620579
25	TAF7	chr3:46620349-46621918	H1-hESC	embryonic stem cell:	n/a	n/a
26	NFIC	chr3:46620297-46620895	ECC-1	luminal epithelium:	n/a	n/a
27	FOXA1	chr3:46620267-46620859	HepG2	liver:	n/a	n/a
28	ARID3A	chr3:46620360-46620882	HepG2	liver:	n/a	n/a
29	NFIC	chr3:46620235-46620962	ECC-1	luminal epithelium:	n/a	n/a
30	BHLHE40	chr3:46620474-46620878	HepG2	liver:	n/a	n/a
31	CHD1	chr3:46617928-46621284	H1-hESC	embryonic stem cell:	n/a	chr3:46619179-46619189
32	TCF7L2	chr3:46620565-46620783	Hela-S3	cervix:	n/a	n/a
33	MYBL2	chr3:46620308-46620857	HepG2	liver:	n/a	n/a
34	POLR2A	chr3:46620465-46622895	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46615629..46619191-chr3:46619379..46621638,3	K562	blood:

Variant related genes	Relation type
TDGF1	TF binding region
ENSG00000241186	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs2280408	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280409	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280410	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2293024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3189859	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3806704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3827493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4312690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55649212	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55693118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55736632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55763532	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55923987	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55955974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55957516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56008703	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56048308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56163098	0.84[AMR][1000 genomes]
rs56168669	0.84[AMR][1000 genomes]
rs56188400	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56197743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56394040	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56398705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56695799	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58177689	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58551379	0.84[AMR][1000 genomes]
rs58572135	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59673973	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59836693	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73069984	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73069987	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73069989	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73069992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73069996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73069997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73071917	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73071919	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73071930	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73071938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73072002	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73073732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73073734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73073742	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73073744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73073745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73073746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73073750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73073752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73073753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73073754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73073755	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73075515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73075519	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075524	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73075528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73075540	0.83[AMR][1000 genomes]
rs73075543	0.83[AMR][1000 genomes]
rs73075564	0.96[AMR][1000 genomes]
rs73075571	0.96[AMR][1000 genomes]
rs73077539	0.84[AMR][1000 genomes]
rs73077544	0.84[AMR][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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46608400-46625400	Weak transcription	Right Atrium	heart
2	chr3:46616800-46620800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr3:46616800-46626600	Weak transcription	Pancreas	Pancrea
4	chr3:46617200-46621600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr3:46617400-46620800	Weak transcription	Gastric	stomach
6	chr3:46617600-46620800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr3:46618200-46620800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:46618200-46622200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr3:46618400-46621000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr3:46618400-46621600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:46618600-46620800	Weak transcription	Lung	lung
12	chr3:46618600-46620800	Weak transcription	Spleen	Spleen
13	chr3:46618800-46624600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:46619800-46621000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr3:46619800-46621200	Enhancers	Dnd41	blood
16	chr3:46620200-46621200	Enhancers	Primary T cells from cord blood	blood
17	chr3:46620200-46621200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr3:46620400-46620800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr3:46620400-46621000	Enhancers	HUVEC	blood vessel
20	chr3:46620400-46621200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr3:46620400-46622800	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
22	chr3:46620400-46622800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
23	chr3:46620400-46622800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
24	chr3:46620400-46623000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
25	chr3:46620400-46624600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:46620600-46620800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr3:46620600-46620800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr3:46620600-46620800	Flanking Active TSS	Stomach Mucosa	stomach
29	chr3:46620600-46621000	Enhancers	Duodenum Mucosa	Duodenum
30	chr3:46620600-46621000	Bivalent Enhancer	K562	blood
31	chr3:46620600-46621200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:46620600-46621200	Enhancers	Left Ventricle	heart
33	chr3:46620600-46621200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
34	chr3:46620600-46621200	Flanking Active TSS	HepG2	liver
35	chr3:46620600-46621400	Enhancers	Liver	Liver
36	chr3:46620600-46621400	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr3:46620600-46621600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:46620600-46622600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:46620600-46622800	Transcr. at gene 5' and 3'	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:46620600-46623400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell

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