Variant report

Variant	rs28625516
Chromosome Location	chr14:24562962-24562963
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	chr14:24562873-24563907	U87	brain:	n/a	n/a
2	TBP	chr14:24562937-24564013	Hela-S3	cervix:	n/a	n/a
3	EP300	chr14:24562957-24564070	K562	blood:	n/a	chr14:24563106-24563120
4	KAP1	chr14:24562941-24563248	U2OS	brain:	n/a	n/a
5	NFYA	chr14:24562919-24563801	Hela-S3	cervix:	n/a	n/a
6	NFIC	chr14:24562915-24565446	HepG2	liver:	n/a	n/a
7	POLR2A	chr14:24562874-24564318	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr14:24562938-24565227	GM18505	blood:	n/a	n/a
9	POLR2A	chr14:24562845-24565052	HL-60	blood:	n/a	n/a
10	MAX	chr14:24562954-24564195	Hela-S3	cervix:	n/a	n/a
11	SIN3AK20	chr14:24562774-24564366	MCF-7	breast:	n/a	n/a
12	ELF1	chr14:24562931-24564983	MCF-7	breast:	n/a	chr14:24563753-24563762 chr14:24563167-24563179 chr14:24563907-24563920
13	HNF4A	chr14:24562866-24563746	HepG2	liver:	n/a	n/a
14	ZNF263	chr14:24562896-24564853	HEK293-T-REx	kidney:	n/a	chr14:24562911-24562920 chr14:24564212-24564221 chr14:24563541-24563550 chr14:24564599-24564608
15	TCF12	chr14:24562946-24564027	ECC-1	luminal epithelium:	n/a	chr14:24563671-24563678
16	ELF1	chr14:24562889-24565311	HepG2	liver:	n/a	chr14:24563753-24563762 chr14:24563167-24563179 chr14:24563907-24563920
17	HEY1	chr14:24562960-24565323	HepG2	liver:	n/a	chr14:24563470-24563485
18	POLR2A	chr14:24562804-24565313	GM12892	blood:	n/a	n/a
19	POLR2A	chr14:24562760-24562964	HCT-116	colon:	n/a	n/a
20	GTF2F1	chr14:24562901-24563956	Hela-S3	cervix:	n/a	n/a
21	FOXM1	chr14:24562775-24564144	MCF-7	breast:	n/a	n/a
22	TAF1	chr14:24562774-24565245	HepG2	liver:	n/a	n/a
23	SP1	chr14:24562766-24563698	H1-hESC	embryonic stem cell:	n/a	chr14:24563358-24563372 chr14:24563281-24563290 chr14:24563281-24563291 chr14:24563280-24563292 chr14:24563282-24563291 chr14:24563277-24563291 chr14:24563282-24563291 chr14:24563351-24563365 chr14:24563463-24563475 chr14:24563128-24563142 chr14:24563281-24563291 chr14:24563280-24563292
24	POLR2A	chr14:24562936-24564029	H1-hESC	embryonic stem cell:	n/a	n/a
25	JUND	chr14:24562934-24564025	MCF-7	breast:	n/a	chr14:24563280-24563289 chr14:24563478-24563487
26	HEY1	chr14:24562819-24565171	K562	blood:	n/a	chr14:24563470-24563485
27	POLR2A	chr14:24562896-24566757	HepG2	liver:	n/a	n/a
28	TCF12	chr14:24562853-24564212	A549	lung:	n/a	chr14:24563671-24563678
29	POLR2A	chr14:24562802-24565389	HCT-116	colon:	n/a	n/a
30	POLR2A	chr14:24562595-24565468	K562	blood:	n/a	n/a
31	POLR2A	chr14:24562763-24566727	HepG2	liver:	n/a	n/a
32	MAX	chr14:24562869-24564147	ECC-1	luminal epithelium:	n/a	n/a
33	POLR2A	chr14:24561955-24565472	H1-hESC	embryonic stem cell:	n/a	n/a
34	YY1	chr14:24562904-24563781	H1-hESC	embryonic stem cell:	n/a	chr14:24563374-24563385 chr14:24563281-24563290 chr14:24563591-24563602 chr14:24563474-24563485 chr14:24563753-24563762
35	ZNF143	chr14:24562958-24563262	H1-hESC	embryonic stem cell:	n/a	n/a
36	ELF1	chr14:24562907-24563660	HepG2	liver:	n/a	chr14:24563167-24563179
37	POLR2A	chr14:24562951-24564035	Hela-S3	cervix:	n/a	n/a
38	EP300	chr14:24562754-24563858	HepG2	liver:	n/a	chr14:24563106-24563120
39	MAX	chr14:24562941-24563832	H1-hESC	embryonic stem cell:	n/a	n/a
40	MBD4	chr14:24562731-24565428	HepG2	liver:	n/a	n/a
41	CEBPB	chr14:24562958-24563438	MCF-7	breast:	n/a	n/a
42	HNF4A	chr14:24562830-24563767	HepG2	liver:	n/a	n/a
43	HCFC1	chr14:24562723-24564191	Hela-S3	cervix:	n/a	n/a
44	MAX	chr14:24562939-24565020	K562	blood:	n/a	chr14:24564836-24564845 chr14:24564833-24564846 chr14:24564830-24564849 chr14:24564833-24564846 chr14:24564834-24564845 chr14:24564835-24564844 chr14:24564835-24564844 chr14:24564835-24564844
45	TEAD4	chr14:24562891-24563289	K562	blood:	n/a	n/a
46	EP300	chr14:24562919-24563652	H1-hESC	embryonic stem cell:	n/a	chr14:24563106-24563120
47	POLR2A	chr14:24562916-24565258	GM12892	blood:	n/a	n/a
48	TBP	chr14:24562881-24565044	H1-hESC	embryonic stem cell:	n/a	n/a
49	HNF4G	chr14:24562951-24563802	HepG2	liver:	n/a	n/a
50	POLR2A	chr14:24562707-24565246	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:24562071..24566278-chr14:24680757..24683932,6	K562	blood:
2	chr14:24561733..24565043-chr14:24622793..24625678,3	K562	blood:
3	chr14:24519494..24523801-chr14:24562244..24565641,8	MCF-7	breast:
4	chr14:24503791..24508058-chr14:24562194..24566408,5	MCF-7	breast:
5	chr14:24562695..24566492-chr14:24599252..24601875,4	MCF-7	breast:
6	chr14:24562501..24566419-chr14:24801112..24803821,3	MCF-7	breast:
7	chr14:24562256..24566141-chr14:24679709..24684040,4	MCF-7	breast:
8	chr14:24562956..24565293-chr14:24631762..24633891,2	MCF-7	breast:
9	chr14:24560776..24564630-chr14:24604018..24609119,8	MCF-7	breast:
10	chr14:24561763..24563268-chr14:24657712..24660361,2	MCF-7	breast:
11	chr14:24562947..24563648-chr2:191878766..191879350,2	HCT-116	colon:
12	chr14:24562071..24566026-chr14:24681194..24683838,4	K562	blood:
13	chr14:24561906..24569428-chr14:24581597..24585823,19	K562	blood:
14	chr14:24562331..24564529-chr14:24910345..24912043,2	K562	blood:
15	chr14:24562455..24565084-chr16:3071701..3074481,2	MCF-7	breast:
16	chr14:24549655..24552374-chr14:24561781..24565761,8	K562	blood:
17	chr14:24549544..24554784-chr14:24561532..24565355,15	MCF-7	breast:
18	chr14:24562336..24564815-chr14:24614686..24617884,3	K562	blood:
19	chr14:24527787..24531306-chr14:24561913..24565086,5	MCF-7	breast:
20	chr14:24560493..24565596-chr14:24608942..24613068,5	K562	blood:
21	chr14:24562089..24565066-chr14:24613987..24617513,5	K562	blood:
22	chr14:24035148..24037025-chr14:24561920..24564742,2	MCF-7	breast:

Variant related genes	Relation type
PCK2	TF binding region
ENSG00000196497	Chromatin interaction
ENSG00000129535	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000139914	Chromatin interaction
ENSG00000100911	Chromatin interaction
ENSG00000131652	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000213928	Chromatin interaction
ENSG00000186648	Chromatin interaction
ENSG00000100897	Chromatin interaction
ENSG00000092098	Chromatin interaction
ENSG00000092010	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000213983	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000100908	Chromatin interaction
ENSG00000225766	Chromatin interaction
ENSG00000259522	Chromatin interaction
ENSG00000115415	Chromatin interaction
ENSG00000259321	Chromatin interaction
ENSG00000103145	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10132601	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10136189	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10136840	1.00[AMR][1000 genomes]
rs10137012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10138006	1.00[EUR][1000 genomes]
rs10138628	1.00[AMR][1000 genomes]
rs10139890	1.00[AMR][1000 genomes]
rs10146394	1.00[AMR][1000 genomes]
rs10147702	1.00[EUR][1000 genomes]
rs10148135	1.00[AMR][1000 genomes]
rs10150403	1.00[AMR][1000 genomes]
rs10151593	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11574504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28420107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28473777	1.00[AMR][1000 genomes]
rs28482359	1.00[AMR][1000 genomes]
rs28528158	1.00[AMR][1000 genomes]
rs28604959	1.00[AMR][1000 genomes]
rs28673535	1.00[AMR][1000 genomes]
rs28674477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28810793	1.00[AMR][1000 genomes]
rs28861824	1.00[AMR][1000 genomes]
rs34861984	1.00[EUR][1000 genomes]
rs55754036	1.00[AMR][1000 genomes]
rs61737105	1.00[EUR][1000 genomes]
rs7151831	1.00[EUR][1000 genomes]
rs74037010	1.00[AMR][1000 genomes]
rs74040010	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3405661	chr14:24189883-24670942	Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv1049316	chr14:24405420-24583724	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv541999	chr14:24405420-24583724	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	esv1827678	chr14:24520544-24663325	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	nsv456168	chr14:24525634-24618859	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv564057	chr14:24525634-24618859	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24551000-24563400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr14:24559600-24563200	Enhancers	Fetal Intestine Large	intestine
3	chr14:24559800-24563000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr14:24559800-24563000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr14:24560000-24563000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr14:24560200-24563000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:24561200-24563000	Enhancers	Psoas Muscle	Psoas
8	chr14:24561200-24563200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr14:24561200-24563200	Enhancers	Pancreas	Pancrea
10	chr14:24561200-24563400	Enhancers	Gastric	stomach
11	chr14:24561200-24563400	Enhancers	Stomach Mucosa	stomach
12	chr14:24561800-24563000	Enhancers	Brain Cingulate Gyrus	brain
13	chr14:24562000-24563000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr14:24562000-24563000	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr14:24562000-24563200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr14:24562200-24563000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr14:24562200-24563000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr14:24562200-24563000	Enhancers	Fetal Brain Female	brain
19	chr14:24562200-24563000	Enhancers	Fetal Muscle Leg	muscle
20	chr14:24562200-24563000	Enhancers	Placenta	Placenta
21	chr14:24562200-24563200	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr14:24562200-24563400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:24562200-24563400	Enhancers	Small Intestine	intestine
24	chr14:24562400-24563000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr14:24562400-24563000	Weak transcription	Brain Substantia Nigra	brain
26	chr14:24562400-24563000	Weak transcription	Osteobl	bone
27	chr14:24562400-24563200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr14:24562400-24563800	Enhancers	Fetal Brain Male	brain
29	chr14:24562600-24563000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:24562600-24563000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr14:24562600-24563000	Enhancers	Primary B cells from cord blood	blood
32	chr14:24562600-24563000	Enhancers	Primary B cells from peripheral blood	blood
33	chr14:24562600-24563000	Enhancers	Primary T cells fromperipheralblood	blood
34	chr14:24562600-24563000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr14:24562600-24563000	Enhancers	Colon Smooth Muscle	Colon
36	chr14:24562600-24563000	Enhancers	Fetal Thymus	thymus
37	chr14:24562600-24563200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr14:24562600-24563200	Enhancers	Lung	lung
39	chr14:24562600-24563400	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr14:24562600-24565000	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr14:24562600-24565200	Active TSS	Rectal Smooth Muscle	rectum
42	chr14:24562800-24563000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr14:24562800-24563000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr14:24562800-24563000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr14:24562800-24563000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr14:24562800-24563000	Enhancers	H9 Cell Line	embryonic stem cell
47	chr14:24562800-24563000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr14:24562800-24563000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr14:24562800-24563000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr14:24562800-24563000	Enhancers	Primary T helper naive cells from peripheral blood	blood

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