Variant report

Variant	rs55955974
Chromosome Location	chr3:46619554-46619555
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	SIN3A	chr3:46617971-46619896	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:46616366-46619569	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF7	chr3:46617846-46619988	H1-hESC	embryonic stem cell:	n/a	n/a
4	TBP	chr3:46618280-46619708	H1-hESC	embryonic stem cell:	n/a	n/a
5	CHD1	chr3:46617928-46621284	H1-hESC	embryonic stem cell:	n/a	chr3:46619179-46619189
6	POLR2A	chr3:46615452-46619820	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: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs2280408	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280409	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280410	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28617572	0.83[ASN][1000 genomes]
rs28687398	0.80[ASN][1000 genomes]
rs3189859	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3827493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4312690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55649212	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55693118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55736632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55763532	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55923987	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55957516	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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];0.94[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];1.00[ASN][1000 genomes]
rs56197743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56394040	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56398705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56695799	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58177689	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58551379	0.84[AMR][1000 genomes]
rs58572135	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59673973	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59836693	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73069984	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73069987	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73069989	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73069992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73069996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73069997	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73071917	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73071919	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73071930	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73071938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73072002	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073742	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73073744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073746	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073752	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73073754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73073755	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73075515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46608400-46625400	Weak transcription	Right Atrium	heart
2	chr3:46615200-46620400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:46616200-46620400	Weak transcription	Stomach Mucosa	stomach
4	chr3:46616600-46620600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:46616800-46620800	Active TSS	H9 Cell Line	embryonic stem cell
6	chr3:46616800-46626600	Weak transcription	Pancreas	Pancrea
7	chr3:46617000-46620600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:46617200-46620600	Weak transcription	Liver	Liver
9	chr3:46617200-46621600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr3:46617400-46620400	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr3:46617400-46620800	Weak transcription	Gastric	stomach
12	chr3:46617600-46620600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr3:46617600-46620800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:46618200-46620400	Active TSS	H1 Cell Line	embryonic stem cell
15	chr3:46618200-46620600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:46618200-46620800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:46618200-46622200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:46618400-46620000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
19	chr3:46618400-46620400	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr3:46618400-46621000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr3:46618400-46621600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
22	chr3:46618600-46620600	Weak transcription	Left Ventricle	heart
23	chr3:46618600-46620800	Weak transcription	Lung	lung
24	chr3:46618600-46620800	Weak transcription	Spleen	Spleen
25	chr3:46618800-46619800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:46618800-46620400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:46618800-46624600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:46619400-46620600	Enhancers	HepG2	liver

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