Variant report

Variant	rs2252725
Chromosome Location	chr15:73586267-73586268
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	FOXA1	chr15:73586116-73586601	HepG2	liver:	n/a	n/a
2	FOXA1	chr15:73586145-73586570	HepG2	liver:	n/a	n/a
3	HNF4A	chr15:73586122-73586524	HepG2	liver:	n/a	chr15:73586278-73586296 chr15:73586279-73586294 chr15:73586281-73586293 chr15:73586280-73586293 chr15:73586322-73586334 chr15:73586320-73586335 chr15:73586280-73586293 chr15:73586280-73586293 chr15:73586322-73586335 chr15:73586280-73586294 chr15:73586322-73586334 chr15:73586281-73586294 chr15:73586279-73586294 chr15:73586280-73586294
4	MAX	chr15:73586055-73586655	HepG2	liver:	n/a	chr15:73586402-73586411
5	SP1	chr15:73586068-73586521	HepG2	liver:	n/a	n/a
6	EP300	chr15:73586057-73586557	HepG2	liver:	n/a	n/a
7	MXI1	chr15:73586195-73586496	HepG2	liver:	n/a	n/a
8	HNF4G	chr15:73586077-73586514	HepG2	liver:	n/a	chr15:73586278-73586296 chr15:73586281-73586293 chr15:73586280-73586293 chr15:73586322-73586334 chr15:73586280-73586293 chr15:73586280-73586293 chr15:73586278-73586293 chr15:73586322-73586335 chr15:73586280-73586294 chr15:73586322-73586334 chr15:73586319-73586334 chr15:73586281-73586294 chr15:73586279-73586294 chr15:73586280-73586294
9	EP300	chr15:73586084-73586515	HepG2	liver:	n/a	n/a
10	HNF4A	chr15:73586077-73586557	HepG2	liver:	n/a	chr15:73586278-73586296 chr15:73586279-73586294 chr15:73586281-73586293 chr15:73586280-73586293 chr15:73586322-73586334 chr15:73586320-73586335 chr15:73586280-73586293 chr15:73586280-73586293 chr15:73586322-73586335 chr15:73586280-73586294 chr15:73586322-73586334 chr15:73586281-73586294 chr15:73586279-73586294 chr15:73586280-73586294
11	MAX	chr15:73586242-73586506	HepG2	liver:	n/a	chr15:73586402-73586411
12	HNF4G	chr15:73586100-73586505	HepG2	liver:	n/a	chr15:73586278-73586296 chr15:73586281-73586293 chr15:73586280-73586293 chr15:73586322-73586334 chr15:73586280-73586293 chr15:73586280-73586293 chr15:73586278-73586293 chr15:73586322-73586335 chr15:73586280-73586294 chr15:73586322-73586334 chr15:73586319-73586334 chr15:73586281-73586294 chr15:73586279-73586294 chr15:73586280-73586294
13	HDAC2	chr15:73586110-73586479	HepG2	liver:	n/a	chr15:73586181-73586195
14	HNF4A	chr15:73586107-73586420	HepG2	liver:	n/a	chr15:73586278-73586296 chr15:73586279-73586294 chr15:73586281-73586293 chr15:73586280-73586293 chr15:73586322-73586334 chr15:73586320-73586335 chr15:73586280-73586293 chr15:73586280-73586293 chr15:73586322-73586335 chr15:73586280-73586294 chr15:73586322-73586334 chr15:73586281-73586294 chr15:73586279-73586294 chr15:73586280-73586294
15	MYC	chr15:73586260-73586444	HepG2	liver:	n/a	chr15:73586402-73586411
16	REST	chr15:73586188-73586452	HepG2	liver:	n/a	n/a
17	FOXA2	chr15:73586144-73586486	HepG2	liver:	n/a	n/a
18	FOXA1	chr15:73586025-73586627	HepG2	liver:	n/a	n/a
19	MYBL2	chr15:73586046-73586603	HepG2	liver:	n/a	chr15:73586286-73586299
20	FOXA1	chr15:73586113-73586521	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73580564..73583381-chr15:73583937..73588117,3	K562	blood:

Variant related genes	Relation type
NEO1	TF binding region
ENSG00000067141	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1017808	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs10438294	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs11072405	0.85[JPT][hapmap]
rs11072411	0.91[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11072412	0.82[ASN][1000 genomes]
rs1119251	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs11634045	0.80[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap]
rs11636981	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs11856537	0.83[CHD][hapmap]
rs12439852	0.81[ASN][1000 genomes]
rs12442755	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap]
rs12594776	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12901272	0.85[JPT][hapmap]
rs1382782	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs1564347	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs1585766	0.85[JPT][hapmap]
rs16957683	0.81[JPT][hapmap]
rs1871385	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1878940	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2292915	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap]
rs2415145	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs2660821	0.87[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2680338	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2680340	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2680341	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34456824	0.81[ASN][1000 genomes]
rs35778649	0.81[ASN][1000 genomes]
rs3736510	0.83[MEX][hapmap];0.83[TSI][hapmap]
rs3743496	0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap]
rs3784795	0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs3859014	0.86[CHB][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs3859015	0.80[CEU][hapmap];0.82[CHB][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap]
rs472681	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4776631	0.80[ASN][1000 genomes]
rs4777592	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs486267	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs489531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs498005	0.80[CHB][hapmap]
rs531019	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs559260	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs563076	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs564765	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs576813	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6495052	0.86[CHD][hapmap]
rs6495053	0.86[CHD][hapmap]
rs6495057	0.86[CHD][hapmap]
rs7177758	0.80[JPT][hapmap]
rs747873	0.81[TSI][hapmap]
rs8039418	0.85[JPT][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	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73535200-73588000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:73536200-73602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:73538000-73593400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:73546800-73588600	Weak transcription	Spleen	Spleen
5	chr15:73552400-73588200	Weak transcription	Hela-S3	cervix
6	chr15:73552800-73598400	Weak transcription	Small Intestine	intestine
7	chr15:73560800-73597200	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr15:73563200-73598600	Weak transcription	Stomach Mucosa	stomach
9	chr15:73563600-73593600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:73566400-73597800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:73568600-73600800	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr15:73570200-73597000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:73570400-73597000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:73571200-73601400	Strong transcription	Fetal Stomach	stomach
15	chr15:73572400-73587600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr15:73574000-73596800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr15:73574800-73588000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:73576000-73586400	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:73576200-73587600	Weak transcription	Right Ventricle	heart
20	chr15:73576400-73594600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:73577800-73586600	Strong transcription	Stomach Smooth Muscle	stomach
22	chr15:73577800-73598200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr15:73578000-73586400	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:73578200-73590600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:73578600-73586400	Strong transcription	Left Ventricle	heart
26	chr15:73579000-73590400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:73579200-73586400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr15:73579200-73598200	Weak transcription	Psoas Muscle	Psoas
29	chr15:73579800-73591400	Strong transcription	Rectal Smooth Muscle	rectum
30	chr15:73580000-73587200	Weak transcription	Colonic Mucosa	Colon
31	chr15:73580400-73594400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:73581600-73598000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:73581800-73588000	Weak transcription	HMEC	breast
34	chr15:73582000-73587600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:73582000-73588200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:73582000-73589400	Weak transcription	Fetal Brain Male	brain
37	chr15:73582000-73590400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:73582000-73590600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr15:73582000-73595200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr15:73582000-73598000	Weak transcription	Fetal Heart	heart
41	chr15:73582200-73589400	Weak transcription	Colon Smooth Muscle	Colon
42	chr15:73582200-73590600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:73582200-73590800	Weak transcription	A549	lung
44	chr15:73582600-73590800	Weak transcription	Fetal Kidney	kidney
45	chr15:73582800-73596800	Strong transcription	Fetal Lung	lung
46	chr15:73583400-73587600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr15:73583400-73587600	Weak transcription	Adipose Nuclei	Adipose
48	chr15:73583400-73588400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:73583400-73589000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:73583400-73590800	Weak transcription	H9 Cell Line	embryonic stem cell

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