Variant report

Variant	rs16976227
Chromosome Location	chr15:55542883-55542884
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	MAX	chr15:55542538-55543076	HepG2	liver:	n/a	chr15:55542753-55542763
2	FOS	chr15:55542560-55543061	MCF10A-Er-Src	breast:	n/a	n/a
3	MAX	chr15:55542615-55542921	K562	blood:	n/a	chr15:55542753-55542763
4	MAX	chr15:55542534-55543051	Hela-S3	cervix:	n/a	chr15:55542753-55542763
5	STAT3	chr15:55542476-55543214	MCF10A-Er-Src	breast:	n/a	chr15:55542803-55542811
6	FOXA1	chr15:55542631-55542937	T-47D	breast:	n/a	chr15:55542768-55542783
7	EP300	chr15:55542608-55543013	K562	blood:	n/a	chr15:55542773-55542783 chr15:55542829-55542843
8	ARID3A	chr15:55542686-55542931	K562	blood:	n/a	n/a
9	MYC	chr15:55542563-55542959	K562	blood:	n/a	chr15:55542753-55542763
10	EP300	chr15:55542615-55542993	HepG2	liver:	n/a	chr15:55542773-55542783 chr15:55542829-55542843
11	GATA3	chr15:55542648-55542981	T-47D	breast:	n/a	n/a
12	MXI1	chr15:55542442-55543171	IMR90	lung:	n/a	n/a
13	CEBPB	chr15:55542546-55543012	MCF-7	breast:	n/a	chr15:55542800-55542813 chr15:55542828-55542839 chr15:55542801-55542812
14	MYC	chr15:55542484-55543064	MCF10A-Er-Src	breast:	n/a	chr15:55542753-55542763
15	CEBPB	chr15:55542482-55543692	Hela-S3	cervix:	n/a	chr15:55543524-55543535 chr15:55542800-55542813 chr15:55542828-55542839 chr15:55543524-55543537 chr15:55542801-55542812
16	RCOR1	chr15:55542814-55543398	K562	blood:	n/a	n/a
17	CEBPB	chr15:55542555-55543721	A549	lung:	n/a	chr15:55543524-55543535 chr15:55542800-55542813 chr15:55542828-55542839 chr15:55543524-55543537 chr15:55542801-55542812
18	NFIC	chr15:55542637-55542964	HepG2	liver:	n/a	n/a
19	FOXA1	chr15:55542617-55543019	HepG2	liver:	n/a	chr15:55542768-55542783
20	FOXA2	chr15:55542581-55542939	HepG2	liver:	n/a	n/a
21	FOXA1	chr15:55542634-55542888	T-47D	breast:	n/a	chr15:55542768-55542783
22	CEBPB	chr15:55542515-55543082	HepG2	liver:	n/a	chr15:55542800-55542813 chr15:55542828-55542839 chr15:55542801-55542812
23	HDAC2	chr15:55542666-55542889	HepG2	liver:	n/a	chr15:55542773-55542782
24	POLR2A	chr15:55542625-55543108	MCF10A-Er-Src	breast:	n/a	n/a
25	FOXA1	chr15:55542559-55542916	HepG2	liver:	n/a	chr15:55542768-55542783
26	CEBPB	chr15:55542655-55542982	HepG2	liver:	n/a	chr15:55542800-55542813 chr15:55542828-55542839 chr15:55542801-55542812
27	ARID3A	chr15:55542492-55543043	HepG2	liver:	n/a	n/a
28	CEBPB	chr15:55542635-55542939	K562	blood:	n/a	chr15:55542800-55542813 chr15:55542828-55542839 chr15:55542801-55542812
29	FOS	chr15:55542570-55543050	MCF10A-Er-Src	breast:	n/a	n/a
30	EP300	chr15:55542515-55543099	Hela-S3	cervix:	n/a	chr15:55542773-55542783 chr15:55542829-55542843
31	FOXA1	chr15:55542439-55542963	HepG2	liver:	n/a	chr15:55542768-55542783
32	FOS	chr15:55542603-55543052	MCF10A-Er-Src	breast:	n/a	n/a
33	MYC	chr15:55542547-55543744	NB4	blood:	n/a	chr15:55542753-55542763
34	CEBPB	chr15:55542581-55543011	IMR90	lung:	n/a	chr15:55542800-55542813 chr15:55542828-55542839 chr15:55542801-55542812
35	GTF2F1	chr15:55542562-55543278	Hela-S3	cervix:	n/a	n/a
36	JUND	chr15:55542696-55542959	K562	blood:	n/a	n/a
37	MYBL2	chr15:55542484-55543011	HepG2	liver:	n/a	n/a
38	TEAD4	chr15:55542551-55543002	HepG2	liver:	n/a	n/a
39	SP1	chr15:55542556-55542977	HepG2	liver:	n/a	n/a
40	TCF12	chr15:55542455-55543087	A549	lung:	n/a	n/a
41	CEBPB	chr15:55542608-55543016	K562	blood:	n/a	chr15:55542800-55542813 chr15:55542828-55542839 chr15:55542801-55542812
42	CEBPB	chr15:55542487-55543148	A549	lung:	n/a	chr15:55542800-55542813 chr15:55542828-55542839 chr15:55542801-55542812
43	SPI1	chr15:55542480-55543651	HL-60	blood:	n/a	chr15:55543297-55543304 chr15:55543294-55543307
44	STAT3	chr15:55542545-55543079	MCF10A-Er-Src	breast:	n/a	chr15:55542803-55542811
45	CHD2	chr15:55542590-55543027	Hela-S3	cervix:	n/a	n/a
46	MAX	chr15:55542561-55543784	NB4	blood:	n/a	chr15:55542753-55542763
47	TCF7L2	chr15:55542607-55542971	Hela-S3	cervix:	n/a	n/a
48	CEBPB	chr15:55542632-55542902	HepG2	liver:	n/a	chr15:55542800-55542813 chr15:55542828-55542839 chr15:55542801-55542812
49	FOS	chr15:55542567-55543061	MCF10A-Er-Src	breast:	n/a	n/a
50	MAX	chr15:55542613-55542909	A549	lung:	n/a	chr15:55542753-55542763

No.	Distal block	Cell Line	Cell type
1	chr15:55542658..55546534-chr15:55547557..55552018,8	K562	blood:
2	chr15:55536038..55538706-chr15:55541637..55544470,3	K562	blood:
3	chr15:55536038..55538985-chr15:55542222..55544123,2	K562	blood:
4	chr15:55538333..55540219-chr15:55542009..55544600,2	MCF-7	breast:
5	chr15:55539059..55540962-chr15:55541694..55543566,2	K562	blood:
6	chr15:55487577..55489204-chr15:55541881..55543410,2	MCF-7	breast:

Variant related genes	Relation type
RAB27A	TF binding region
ENSG00000137876	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10518805	1.00[CEU][hapmap]
rs12324754	0.81[EUR][1000 genomes]
rs12324775	0.81[EUR][1000 genomes]
rs12439213	1.00[CEU][hapmap]
rs12439890	1.00[CEU][hapmap]
rs12440497	1.00[CEU][hapmap]
rs12440550	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12441258	1.00[CEU][hapmap]
rs12442937	1.00[CEU][hapmap]
rs16976218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238178	1.00[CEU][hapmap]
rs17238220	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819000	1.00[CEU][hapmap]
rs17819012	1.00[CEU][hapmap]
rs28499877	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28705006	0.90[EUR][1000 genomes]
rs557254	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7170936	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177930	1.00[CEU][hapmap]
rs8039254	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9920531	1.00[CEU][hapmap];1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv1049977	chr15:55502508-55555694	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1036924	chr15:55527874-55616480	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv569522	chr15:55532211-55611126	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv904241	chr15:55534342-55611126	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55490000-55562800	Weak transcription	Ovary	ovary
2	chr15:55514200-55545200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:55514600-55543200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:55514800-55560400	Weak transcription	Spleen	Spleen
5	chr15:55516000-55559600	Weak transcription	Fetal Stomach	stomach
6	chr15:55520800-55574800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:55522800-55543200	Weak transcription	Pancreas	Pancrea
8	chr15:55522800-55547000	Weak transcription	GM12878-XiMat	blood
9	chr15:55526800-55543200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:55527000-55544200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:55533800-55543400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr15:55534400-55545600	Weak transcription	Osteobl	bone
13	chr15:55537200-55543200	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr15:55538600-55544200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:55538600-55549000	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr15:55538800-55544600	Genic enhancers	K562	blood
17	chr15:55539000-55543800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr15:55539000-55544600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr15:55539400-55544600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr15:55539600-55544400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:55539800-55545000	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr15:55540000-55544400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr15:55540600-55545000	Enhancers	Liver	Liver
24	chr15:55540600-55561200	Weak transcription	Esophagus	oesophagus
25	chr15:55540800-55543600	Enhancers	Fetal Lung	lung
26	chr15:55541000-55544200	Enhancers	Placenta	Placenta
27	chr15:55541200-55549000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:55541400-55543400	Enhancers	HepG2	liver
29	chr15:55541400-55544800	Enhancers	Stomach Mucosa	stomach
30	chr15:55541400-55547200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr15:55541600-55543800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr15:55541600-55543800	Enhancers	Small Intestine	intestine
33	chr15:55541600-55544200	Enhancers	Primary hematopoietic stem cells	blood
34	chr15:55541600-55544800	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr15:55541600-55545600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:55541600-55545800	Enhancers	Primary T cells fromperipheralblood	blood
37	chr15:55541800-55543000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr15:55541800-55543200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:55541800-55544200	Enhancers	Primary B cells from cord blood	blood
40	chr15:55541800-55544600	Enhancers	Primary T cells from cord blood	blood
41	chr15:55541800-55547800	Weak transcription	Left Ventricle	heart
42	chr15:55542000-55543600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:55542000-55544200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr15:55542000-55545800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr15:55542200-55543000	Weak transcription	Colonic Mucosa	Colon
46	chr15:55542200-55543200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:55542200-55543400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr15:55542200-55543800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:55542200-55543800	Enhancers	Fetal Thymus	thymus
50	chr15:55542200-55544400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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