Variant report

Variant	rs2280414
Chromosome Location	chr3:46621215-46621216
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	POLR2A	chr3:46621057-46621328	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF7L2	chr3:46620294-46621228	HepG2	liver:	n/a	chr3:46620308-46620322
3	ATF2	chr3:46620946-46621548	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:46620911-46621575	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr3:46620748-46621730	H1-hESC	embryonic stem cell:	n/a	n/a
6	SIN3A	chr3:46620390-46621386	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:46620992-46621571	H1-hESC	embryonic stem cell:	n/a	n/a
8	TAF7	chr3:46620349-46621918	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD1	chr3:46617928-46621284	H1-hESC	embryonic stem cell:	n/a	chr3:46619179-46619189
10	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: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs13070740	1.00[MKK][hapmap]
rs13093282	1.00[MKK][hapmap]
rs17286758	0.81[CHB][hapmap]
rs2176862	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs2280408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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]
rs55955974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
rs6442003	0.81[CHB][hapmap]
rs6772291	0.81[CHB][hapmap]
rs6778422	0.81[CHB][hapmap]
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]
rs7648827	0.81[CHB][hapmap]
rs9808967	0.81[CHB][hapmap]
rs9846026	0.81[CHB][hapmap]
rs9871405	0.81[CHB][hapmap]

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:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46608400-46625400	Weak transcription	Right Atrium	heart
2	chr3:46616800-46626600	Weak transcription	Pancreas	Pancrea
3	chr3:46617200-46621600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:46618200-46622200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:46618400-46621600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:46618800-46624600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:46620400-46622800	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
8	chr3:46620400-46622800	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
9	chr3:46620400-46622800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
10	chr3:46620400-46623000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
11	chr3:46620400-46624600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:46620600-46621400	Enhancers	Liver	Liver
13	chr3:46620600-46621400	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr3:46620600-46621600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:46620600-46622600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:46620600-46622800	Transcr. at gene 5' and 3'	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:46620600-46623400	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
18	chr3:46620800-46621400	Enhancers	Gastric	stomach
19	chr3:46620800-46621400	Enhancers	Lung	lung
20	chr3:46620800-46622400	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:46620800-46622600	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
22	chr3:46620800-46622600	Enhancers	Stomach Mucosa	stomach
23	chr3:46620800-46622800	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
24	chr3:46621000-46621600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:46621000-46621600	Bivalent Enhancer	Fetal Thymus	thymus
26	chr3:46621000-46622600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
27	chr3:46621000-46627200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:46621200-46621600	Flanking Active TSS	Colonic Mucosa	Colon
29	chr3:46621200-46622000	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr3:46621200-46622200	Weak transcription	Spleen	Spleen
31	chr3:46621200-46622600	Enhancers	HepG2	liver
32	chr3:46621200-46626200	Weak transcription	Dnd41	blood

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