Variant report

Variant	rs28454221
Chromosome Location	chr15:57592085-57592086
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	EGR1	chr15:57591946-57592185	K562	blood:	n/a	chr15:57592079-57592092 chr15:57592040-57592053 chr15:57592041-57592055 chr15:57592080-57592094 chr15:57592081-57592091
2	MXI1	chr15:57591929-57592376	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:57591968-57592541	GM12878	blood:	n/a	n/a
4	EGR1	chr15:57591922-57592208	GM12878	blood:	n/a	chr15:57592079-57592092 chr15:57592040-57592053 chr15:57592041-57592055 chr15:57592080-57592094 chr15:57592081-57592091
5	RUNX3	chr15:57591661-57592548	GM12878	blood:	n/a	n/a
6	REST	chr15:57591875-57592571	HL-60	blood:	n/a	n/a
7	WRNIP1	chr15:57591555-57592415	GM12878	blood:	n/a	n/a
8	RELA	chr15:57591857-57592952	GM15510	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
9	EGR1	chr15:57591962-57592178	GM12878	blood:	n/a	chr15:57592079-57592092 chr15:57592040-57592053 chr15:57592041-57592055 chr15:57592080-57592094 chr15:57592081-57592091
10	POLR2A	chr15:57591886-57592570	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr15:57592012-57592483	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:57591980-57592597	GM12892	blood:	n/a	n/a
13	EP300	chr15:57592033-57592367	GM12878	blood:	n/a	chr15:57592079-57592095
14	POLR2A	chr15:57591063-57592554	HL-60	blood:	n/a	n/a
15	NRF1	chr15:57592068-57592399	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:57592082-57592518	GM12878	blood:	n/a	n/a
17	EP300	chr15:57591954-57592481	GM12878	blood:	n/a	chr15:57592079-57592095
18	POLR2A	chr15:57592054-57592160	HUVEC	blood vessel:	n/a	n/a
19	BCLAF1	chr15:57591895-57592484	GM12878	blood:	n/a	chr15:57592091-57592104 chr15:57592122-57592131
20	TAF1	chr15:57591960-57592556	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:57591325-57596303	NB4	blood:	n/a	n/a
22	SPI1	chr15:57592035-57592275	GM12878	blood:	n/a	n/a
23	SPI1	chr15:57591941-57592376	GM12891	blood:	n/a	n/a
24	ZNF384	chr15:57591999-57592860	GM12878	blood:	n/a	n/a
25	MAX	chr15:57591131-57593104	NB4	blood:	n/a	n/a
26	MYC	chr15:57591905-57593043	NB4	blood:	n/a	n/a
27	RELA	chr15:57591673-57593287	GM19193	blood:	n/a	chr15:57592123-57592132 chr15:57592123-57592132
28	EBF1	chr15:57591958-57592470	GM12878	blood:	n/a	n/a
29	NFIC	chr15:57591896-57592485	GM12878	blood:	n/a	n/a
30	MTA3	chr15:57591568-57592581	GM12878	blood:	n/a	n/a
31	EBF1	chr15:57591953-57592476	GM12878	blood:	n/a	n/a
32	FOXM1	chr15:57591850-57592399	GM12878	blood:	n/a	n/a
33	POLR2A	chr15:57591446-57594099	GM12891	blood:	n/a	n/a
34	NFIC	chr15:57591827-57592573	GM12878	blood:	n/a	n/a
35	ELF1	chr15:57591934-57592562	GM12878	blood:	n/a	n/a
36	SPI1	chr15:57591905-57592406	GM12878	blood:	n/a	n/a
37	POLR2A	chr15:57591978-57592481	GM12878	blood:	n/a	n/a
38	STAT5A	chr15:57591883-57592495	GM12878	blood:	n/a	chr15:57592264-57592271
39	POLR2A	chr15:57591872-57592914	GM19099	blood:	n/a	n/a
40	STAT3	chr15:57592039-57592506	GM12878	blood:	n/a	chr15:57592264-57592271
41	FOXM1	chr15:57591932-57592585	GM12878	blood:	n/a	n/a
42	BHLHE40	chr15:57591928-57593506	GM12878	blood:	n/a	n/a
43	IRF4	chr15:57591976-57592464	GM12878	blood:	n/a	n/a
44	ZNF143	chr15:57591983-57592511	GM12878	blood:	n/a	n/a
45	CEBPB	chr15:57591671-57592095	K562	blood:	n/a	chr15:57591855-57591864 chr15:57591853-57591866 chr15:57591853-57591864
46	POU2F2	chr15:57591865-57592711	GM12878	blood:	n/a	n/a
47	SP1	chr15:57591928-57592552	GM12878	blood:	n/a	n/a
48	ATF2	chr15:57591803-57592469	GM12878	blood:	n/a	n/a
49	MAX	chr15:57591922-57592482	GM12878	blood:	n/a	n/a
50	STAT1	chr15:57591938-57592349	GM12878	blood:	n/a	chr15:57592264-57592271

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:57592040-57592090	HRCEpiC	kidney:	n/a
2	chr15:57592083-57592133	HAEpiC	amniotic membrane:	n/a
3	chr15:57592083-57592133	SK-N-MC	brain:	n/a
4	chr15:57592040-57592090	HEEpiC	esophagus:	n/a
5	chr15:57592083-57592133	LNCaP	prostate:	n/a
6	chr15:57592083-57592133	HepG2	liver:	n/a
7	chr15:57592040-57592090	HRPEpiC	eye:	n/a
8	chr15:57592040-57592090	HNPCEpiC	eye:	n/a
9	chr15:57592083-57592133	HCPEpiC	choroid plexus:	n/a
10	chr15:57592040-57592090	SAEC	small airway:	n/a
11	chr15:57592040-57592090	GM19239	blood:	n/a
12	chr15:57592040-57592090	AG04449	skin:	fetal
13	chr15:57592040-57592090	HPAEpiC	pulmonary alveolar:	n/a
14	chr15:57592040-57592090	PANC-1	pancreas:	n/a
15	chr15:57592040-57592090	HepG2	liver:	n/a
16	chr15:57592040-57592090	HEK293	kidney:	embryo
17	chr15:57592083-57592133	AG09309	skin:	n/a
18	chr15:57592040-57592090	HCM	heart:	n/a
19	chr15:57592040-57592090	AG10803	skin:	n/a
20	chr15:57592083-57592133	SKMC	muscle:	n/a
21	chr15:57592040-57592090	HCF	heart:	n/a
22	chr15:57592083-57592133	AG09319	gingival:	n/a
23	chr15:57592040-57592090	HIPEpiC	eye:	n/a
24	chr15:57592083-57592133	PrEC	prostate:	n/a
25	chr15:57592083-57592133	NHBE	bronchial:	n/a
26	chr15:57592040-57592090	A549	lung:	n/a
27	chr15:57592040-57592090	SK-N-SH	brain:	n/a
28	chr15:57592040-57592090	AG09309	skin:	n/a
29	chr15:57592040-57592090	IMR90	lung:	fetal
30	chr15:57592040-57592090	PFSK-1	brain:	n/a
31	chr15:57592083-57592133	MCF-7	breast:	n/a
32	chr15:57592040-57592090	T-47D	breast:	n/a
33	chr15:57592083-57592133	Hepatocyte	liver:	n/a
34	chr15:57592083-57592133	NH-A	brain:	n/a
35	chr15:57592040-57592090	NH-A	brain:	n/a
36	chr15:57592083-57592133	U87	brain:	n/a
37	chr15:57592040-57592090	ovcar-3	ovarian:	n/a
38	chr15:57592040-57592090	Caco-2	colon:	n/a
39	chr15:57592083-57592133	GM19239	blood:	n/a
40	chr15:57592083-57592133	AG04450	lung:	fetal
41	chr15:57592040-57592090	NB4	blood:	n/a
42	chr15:57592040-57592090	NT2-D1	testis:	n/a
43	chr15:57592040-57592090	U87	brain:	n/a
44	chr15:57592083-57592133	HRE	kidney:	n/a
45	chr15:57592040-57592090	SK-N-MC	brain:	n/a
46	chr15:57592083-57592133	HEK293	kidney:	embryo
47	chr15:57592083-57592133	NB4	blood:	n/a
48	chr15:57592040-57592090	HCT-116	colon:	n/a
49	chr15:57592040-57592090	MCF-7	breast:	n/a
50	chr15:57592083-57592133	GM12892	blood:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:114709342..114710106-chr15:57591884..57592412,2	NB4	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCF12-1	chr15:57592039-57593122	XLOC_011264
2	lnc-TCF12-1	chr15:57592039-57593122	XLOC_011264

Variant related genes	Relation type
LINC00926	TF binding region
LINC00926	CpG island
ENSG00000148737	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1045665	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10518898	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10518904	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16953323	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977245	1.00[EUR][1000 genomes]
rs16977253	1.00[EUR][1000 genomes]
rs16977272	1.00[EUR][1000 genomes]
rs16977276	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977280	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977284	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977297	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977308	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977312	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977315	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977329	1.00[EUR][1000 genomes]
rs16977330	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977333	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977341	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977352	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977353	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977354	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16977372	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1867639	1.00[EUR][1000 genomes]
rs2593220	1.00[EUR][1000 genomes]
rs2615251	1.00[EUR][1000 genomes]
rs2733316	1.00[EUR][1000 genomes]
rs2733317	1.00[EUR][1000 genomes]
rs2733343	1.00[EUR][1000 genomes]
rs2733345	1.00[EUR][1000 genomes]
rs935327	1.00[EUR][1000 genomes]
rs935329	1.00[EUR][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	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv526342	chr15:57565859-57597280	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
2	chr15:57578600-57598200	Weak transcription	Right Ventricle	heart
3	chr15:57578800-57592800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr15:57579200-57592800	Weak transcription	Small Intestine	intestine
5	chr15:57579600-57598200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:57579800-57595000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:57580000-57598400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr15:57580000-57598400	Weak transcription	Fetal Brain Male	brain
9	chr15:57580000-57598400	Weak transcription	NHEK	skin
10	chr15:57580600-57594800	Weak transcription	HepG2	liver
11	chr15:57581600-57595000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr15:57583400-57595000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:57583400-57598400	Weak transcription	Thymus	Thymus
14	chr15:57583600-57598000	Weak transcription	Liver	Liver
15	chr15:57583600-57598200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr15:57583600-57598400	Weak transcription	A549	lung
17	chr15:57583800-57595400	Weak transcription	Aorta	Aorta
18	chr15:57583800-57596800	Weak transcription	Fetal Intestine Large	intestine
19	chr15:57584000-57598200	Weak transcription	Brain Germinal Matrix	brain
20	chr15:57584400-57598000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:57584400-57598200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr15:57584600-57594600	Weak transcription	Primary T cells from cord blood	blood
23	chr15:57584600-57598200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:57584600-57598200	Weak transcription	Fetal Stomach	stomach
25	chr15:57585000-57598400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:57585600-57598000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:57585800-57598200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:57588400-57593000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr15:57589200-57598200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:57589400-57592400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:57589400-57594800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:57589400-57595000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:57589400-57598200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:57589400-57598200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:57589600-57595200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr15:57589600-57598200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:57589600-57598400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:57589800-57592800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:57590000-57592800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:57590000-57597000	Weak transcription	Fetal Intestine Small	intestine
41	chr15:57590000-57598200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:57590000-57598200	Weak transcription	Pancreas	Pancrea
43	chr15:57590400-57592400	Enhancers	Fetal Lung	lung
44	chr15:57590400-57593600	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr15:57590800-57592400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:57590800-57598200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr15:57591000-57592200	Enhancers	Fetal Muscle Leg	muscle
48	chr15:57591000-57592400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr15:57591000-57592400	Enhancers	Fetal Muscle Trunk	muscle
50	chr15:57591000-57592400	Enhancers	Ovary	ovary

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