Variant report

Variant	rs28365901
Chromosome Location	chr15:59396977-59396978
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	chr15:59396947-59398392	Hela-S3	cervix:	n/a	n/a
2	CREB1	chr15:59396969-59397398	A549	lung:	n/a	n/a
3	POLR2A	chr15:59396926-59398071	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:59396668-59398091	PANC-1	pancreas:	n/a	n/a
5	MAX	chr15:59396974-59397981	K562	blood:	n/a	n/a
6	POLR2A	chr15:59396862-59398001	K562	blood:	n/a	n/a
7	MAX	chr15:59396818-59398191	ECC-1	luminal epithelium:	n/a	n/a
8	SP1	chr15:59396794-59397785	A549	lung:	n/a	chr15:59397701-59397710 chr15:59397702-59397715 chr15:59397221-59397242 chr15:59397254-59397275
9	POLR2A	chr15:59396864-59398367	HepG2	liver:	n/a	n/a
10	TAF1	chr15:59396897-59397928	SK-N-SH	brain:	n/a	n/a
11	MAX	chr15:59396879-59398114	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr15:59396851-59398109	PFSK-1	brain:	n/a	n/a
13	CHD2	chr15:59396921-59397965	K562	blood:	n/a	n/a
14	E2F4	chr15:59396946-59397909	K562	blood:	n/a	chr15:59397222-59397231
15	MXI1	chr15:59396594-59398951	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr15:59396959-59397912	Gliobla	brain:	n/a	n/a
17	POLR2A	chr15:59396917-59397895	H1-hESC	embryonic stem cell:	n/a	n/a
18	FOXA2	chr15:59396974-59397822	A549	lung:	n/a	n/a
19	POLR2A	chr15:59396902-59397990	K562	blood:	n/a	n/a
20	POLR2A	chr15:59396793-59397957	Raji	blood:	n/a	n/a
21	REST	chr15:59396825-59398140	A549	lung:	n/a	chr15:59397337-59397344 chr15:59397634-59397647 chr15:59397634-59397647
22	POLR2A	chr15:59396865-59398240	PBDE	blood:	n/a	n/a
23	STAT5A	chr15:59396783-59397666	GM12878	blood:	n/a	n/a
24	MAX	chr15:59396859-59398038	K562	blood:	n/a	n/a
25	PML	chr15:59396860-59397598	K562	blood:	n/a	n/a
26	POLR2A	chr15:59396902-59397955	GM19099	blood:	n/a	n/a
27	POLR2A	chr15:59396952-59397982	ProgFib	skin:	n/a	n/a
28	POLR2A	chr15:59396931-59398066	MCF10A-Er-Src	breast:	n/a	n/a
29	TAF1	chr15:59396922-59398121	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr15:59396963-59397976	K562	blood:	n/a	n/a
31	SIN3AK20	chr15:59396745-59398175	MCF-7	breast:	n/a	n/a
32	TBL1XR1	chr15:59396879-59397551	GM12878	blood:	n/a	n/a
33	MYC	chr15:59396786-59397985	NB4	blood:	n/a	n/a
34	POLR2A	chr15:59396874-59397968	K562	blood:	n/a	n/a
35	SP1	chr15:59396826-59398082	A549	lung:	n/a	chr15:59397701-59397710 chr15:59397702-59397715 chr15:59397221-59397242 chr15:59397254-59397275
36	POLR2A	chr15:59396809-59398092	HUVEC	blood vessel:	n/a	n/a
37	SP1	chr15:59396962-59397581	GM12878	blood:	n/a	chr15:59397221-59397242 chr15:59397254-59397275
38	POLR2A	chr15:59396925-59397980	K562	blood:	n/a	n/a
39	TAF1	chr15:59396849-59398001	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr15:59396946-59397824	HepG2	liver:	n/a	n/a
41	CBX3	chr15:59396833-59397888	K562	blood:	n/a	n/a
42	POLR2A	chr15:59396793-59397943	MCF10A-Er-Src	breast:	n/a	n/a
43	TCF7L2	chr15:59396924-59398305	Hela-S3	cervix:	n/a	chr15:59398184-59398200 chr15:59398188-59398197 chr15:59398184-59398198 chr15:59398187-59398196 chr15:59398184-59398200 chr15:59398186-59398196 chr15:59398185-59398199
44	TAF1	chr15:59396915-59398027	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr15:59396974-59397858	GM12878	blood:	n/a	n/a
46	TAF1	chr15:59396908-59397885	H1-hESC	embryonic stem cell:	n/a	n/a
47	FOXM1	chr15:59396671-59398128	SK-N-SH	brain:	n/a	n/a
48	RUNX3	chr15:59396881-59397540	GM12878	blood:	n/a	n/a
49	NFYB	chr15:59396888-59397803	K562	blood:	n/a	chr15:59397220-59397234 chr15:59397253-59397268 chr15:59397255-59397265 chr15:59397220-59397235 chr15:59397253-59397268 chr15:59397250-59397265 chr15:59397253-59397267 chr15:59397220-59397235 chr15:59397219-59397231 chr15:59397222-59397232
50	CUX1	chr15:59396950-59397174	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:166808599..166809122-chr15:59396935..59397740,2	Hela-S3	cervix:
2	chr10:94449635..94450319-chr15:59396946..59397778,2	NB4	blood:
3	chr15:59277958..59282108-chr15:59396207..59399778,7	K562	blood:
4	chr15:59396782..59397758-chr2:151343358..151344154,2	Hela-S3	cervix:
5	chr15:59395795..59398698-chr15:59981439..59982956,2	K562	blood:
6	chr15:59223805..59226728-chr15:59396182..59398979,2	MCF-7	breast:
7	chr15:59223596..59226559-chr15:59396307..59399219,5	K562	blood:
8	chr15:59224236..59226559-chr15:59396307..59398942,5	K562	blood:
9	chr12:51476647..51477383-chr15:59396869..59397844,2	Hela-S3	cervix:
10	chr15:59396809..59397470-chr2:25016107..25016774,2	HCT-116	colon:
11	chr15:59396643..59397820-chr6:27100194..27101399,3	Hela-S3	cervix:

Variant related genes	Relation type
CCNB2	TF binding region
ENSG00000184924	Chromatin interaction
ENSG00000140299	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000115963	Chromatin interaction
ENSG00000152804	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000143157	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000157450	Chromatin interaction
ENSG00000138092	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11071408	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs12438949	1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12441365	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs12443442	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16941030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16941042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16941046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16941051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16941055	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16941063	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16941069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16953412	0.86[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[TSI][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044436	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2414620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28376133	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383490	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383497	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383502	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383504	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383512	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383514	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383519	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383520	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383523	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383531	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383536	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383542	0.86[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[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383549	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383552	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383553	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383561	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28399204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28406885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28491732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615244	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28739024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751538	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3764193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803449	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809531	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4523870	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4775132	1.00[MEX][hapmap]
rs56187627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56294483	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56891889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57057009	0.83[EUR][1000 genomes]
rs57750394	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57803886	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58014933	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58207484	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58321899	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58827061	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59037515	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59398329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59921711	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60533405	0.83[EUR][1000 genomes]
rs60628647	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60785075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61369543	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61690344	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7165934	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73418826	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73418890	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73418896	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74017339	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74017345	0.83[EUR][1000 genomes]
rs74017356	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74017357	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8035850	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8043536	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59377200-59397000	Weak transcription	Gastric	stomach
2	chr15:59385800-59397000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:59385800-59397400	Weak transcription	Spleen	Spleen
4	chr15:59389200-59397200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:59394000-59397200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:59396400-59397000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
7	chr15:59396400-59397200	Flanking Active TSS	Dnd41	blood
8	chr15:59396600-59397000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr15:59396600-59397000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr15:59396600-59397000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr15:59396600-59397000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr15:59396600-59397000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:59396600-59397000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr15:59396600-59397000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr15:59396600-59397000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr15:59396600-59397000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:59396600-59397000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
18	chr15:59396600-59397000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr15:59396600-59397000	Flanking Active TSS	HSMM	muscle
20	chr15:59396600-59397000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr15:59396600-59397200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:59396600-59397200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr15:59396600-59397400	Active TSS	Stomach Smooth Muscle	stomach
24	chr15:59396600-59397600	Active TSS	Thymus	Thymus
25	chr15:59396600-59397800	Active TSS	Brain Anterior Caudate	brain
26	chr15:59396600-59397800	Active TSS	Brain Cingulate Gyrus	brain
27	chr15:59396600-59397800	Active TSS	Brain Substantia Nigra	brain
28	chr15:59396600-59398000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:59396600-59398000	Active TSS	Brain Hippocampus Middle	brain
30	chr15:59396600-59398000	Active TSS	Rectal Smooth Muscle	rectum
31	chr15:59396600-59398400	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr15:59396600-59398400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:59396600-59398400	Active TSS	Fetal Kidney	kidney
34	chr15:59396600-59398400	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr15:59396600-59398600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:59396600-59398800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:59396600-59398800	Active TSS	A549	lung
38	chr15:59396600-59398800	Active TSS	K562	blood
39	chr15:59396600-59399400	Active TSS	NHDF-Ad	bronchial
40	chr15:59396800-59397000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr15:59396800-59397000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr15:59396800-59397000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr15:59396800-59397000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr15:59396800-59397000	Active TSS	Primary B cells from cord blood	blood
45	chr15:59396800-59397000	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr15:59396800-59397000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr15:59396800-59397000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:59396800-59397000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:59396800-59397000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:59396800-59397000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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