Variant report

Variant	rs4000713
Chromosome Location	chr7:25990597-25990598
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	SIN3A	chr7:25989265-25991735	H1-hESC	embryonic stem cell:	n/a	chr7:25990195-25990206 chr7:25990193-25990206 chr7:25991169-25991182 chr7:25990724-25990737 chr7:25991166-25991175 chr7:25991177-25991190 chr7:25990883-25990894
2	POLR2A	chr7:25985526-25991809	GM19099	blood:	n/a	n/a
3	HDAC2	chr7:25990493-25991493	MCF-7	breast:	n/a	chr7:25990768-25990776
4	POLR2A	chr7:25990526-25990934	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr7:25990502-25991297	K562	blood:	n/a	chr7:25990861-25990876 chr7:25990831-25990840 chr7:25990577-25990587
6	TAF1	chr7:25990531-25991010	ECC-1	luminal epithelium:	n/a	n/a
7	NFYB	chr7:25990571-25991005	K562	blood:	n/a	chr7:25990817-25990827 chr7:25990814-25990829 chr7:25990814-25990829 chr7:25990815-25990829
8	ETS1	chr7:25990585-25990863	K562	blood:	n/a	chr7:25990621-25990634 chr7:25990829-25990840
9	SIN3AK20	chr7:25989901-25990600	H1-hESC	embryonic stem cell:	n/a	n/a
10	REST	chr7:25990383-25991013	HL-60	blood:	n/a	chr7:25990724-25990737 chr7:25990870-25990883
11	MAX	chr7:25990136-25991357	HepG2	liver:	n/a	chr7:25990932-25990943 chr7:25991249-25991259
12	POLR2A	chr7:25990545-25991348	HEK293	kidney:	n/a	n/a
13	MAX	chr7:25989822-25991418	H1-hESC	embryonic stem cell:	n/a	chr7:25990932-25990943 chr7:25991249-25991259
14	YY1	chr7:25990525-25990979	GM12878	blood:	n/a	chr7:25990683-25990697 chr7:25990671-25990685
15	CHD2	chr7:25990274-25991363	GM12878	blood:	n/a	chr7:25990731-25990741 chr7:25990920-25990930 chr7:25990411-25990421
16	MAX	chr7:25990528-25991540	MCF-7	breast:	n/a	chr7:25990932-25990943 chr7:25991249-25991259
17	HEY1	chr7:25990589-25990950	K562	blood:	n/a	n/a
18	POLR2A	chr7:25990549-25990818	HepG2	liver:	n/a	n/a
19	POLR2A	chr7:25990555-25990985	HCT-116	colon:	n/a	n/a
20	TCF12	chr7:25990587-25991450	ECC-1	luminal epithelium:	n/a	n/a
21	FOXP2	chr7:25990536-25991281	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr7:25987021-25992694	HepG2	liver:	n/a	n/a
23	POLR2A	chr7:25986974-25991365	HepG2	liver:	n/a	n/a
24	CREB1	chr7:25989239-25991492	HepG2	liver:	n/a	n/a
25	POLR2A	chr7:25989708-25991441	HL-60	blood:	n/a	n/a
26	YY1	chr7:25990488-25990981	H1-hESC	embryonic stem cell:	n/a	chr7:25990683-25990697 chr7:25990671-25990685
27	POLR2A	chr7:25990573-25991458	GM12891	blood:	n/a	n/a
28	TEAD4	chr7:25990573-25991032	ECC-1	luminal epithelium:	n/a	n/a
29	CREB1	chr7:25990575-25991022	K562	blood:	n/a	n/a
30	POLR2A	chr7:25989404-25990965	K562	blood:	n/a	n/a
31	YY1	chr7:25990546-25990954	HepG2	liver:	n/a	chr7:25990683-25990697 chr7:25990671-25990685
32	MXI1	chr7:25990585-25991346	HepG2	liver:	n/a	n/a
33	YY1	chr7:25990539-25991010	ECC-1	luminal epithelium:	n/a	chr7:25990683-25990697 chr7:25990671-25990685
34	TCF7L2	chr7:25990575-25991329	HCT-116	colon:	n/a	n/a
35	CREB1	chr7:25990591-25991000	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr7:25990245-25990950	K562	blood:	n/a	n/a
37	POLR2A	chr7:25986274-25991748	GM18526	blood:	n/a	n/a
38	POLR2A	chr7:25990592-25991465	MCF-7	breast:	n/a	n/a
39	POLR2A	chr7:25990557-25990960	K562	blood:	n/a	n/a
40	TAF1	chr7:25989818-25990968	H1-hESC	embryonic stem cell:	n/a	n/a
41	UBTF	chr7:25990517-25990862	K562	blood:	n/a	n/a
42	MAX	chr7:25989202-25990609	H1-hESC	embryonic stem cell:	n/a	n/a
43	PAX5	chr7:25990511-25990981	GM12892	blood:	n/a	chr7:25990847-25990856
44	POLR2A	chr7:25990218-25991696	MCF-7	breast:	n/a	n/a
45	MYC	chr7:25990003-25991087	K562	blood:	n/a	chr7:25990932-25990943
46	CHD2	chr7:25990163-25991357	HepG2	liver:	n/a	chr7:25990731-25990741 chr7:25990920-25990930 chr7:25990411-25990421
47	POLR2A	chr7:25990500-25990975	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr7:25990524-25990967	K562	blood:	n/a	n/a
49	ZBTB7A	chr7:25989942-25990985	K562	blood:	n/a	chr7:25990625-25990636 chr7:25990624-25990635
50	POLR2A	chr7:25985030-25991406	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:25932775..25935474-chr7:25989853..25992220,2	K562	blood:
2	chr7:25990509..25992566-chr7:25994471..25996898,2	K562	blood:
3	chr7:25990207..25991830-chr7:26094178..26097069,2	MCF-7	breast:
4	chr7:25965773..25968588-chr7:25989969..25992378,2	MCF-7	breast:
5	chr7:25990038..25992521-chr7:26240210..26242861,2	MCF-7	breast:
6	chr7:25990295..25993400-chr7:26020103..26023231,3	MCF-7	breast:
7	chr7:25990219..25991822-chr7:25999068..26002038,2	K562	blood:
8	chr7:25989265..25991851-chr7:26238825..26240746,4	MCF-7	breast:
9	chr7:25901871..25903514-chr7:25989852..25991943,2	K562	blood:
10	chr7:25989811..25992726-chr7:26096097..26097704,2	MCF-7	breast:
11	chr7:25901385..25904121-chr7:25989908..25991928,2	MCF-7	breast:
12	chr7:25990548..25994647-chr7:26001939..26005377,4	MCF-7	breast:
13	chr7:25952760..25954350-chr7:25989892..25992459,2	K562	blood:
14	chr7:25990246..25992488-chr7:26100564..26102799,3	MCF-7	breast:

Variant related genes	Relation type
MIR148A	TF binding region
ENSG00000270933	TF binding region
ENSG00000122566	Chromatin interaction
ENSG00000122565	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11760762	0.82[ASN][1000 genomes]
rs12700679	0.82[ASN][1000 genomes]
rs12700680	0.82[ASN][1000 genomes]
rs12700681	0.82[ASN][1000 genomes]
rs12700682	0.82[ASN][1000 genomes]
rs13226851	0.82[ASN][1000 genomes]
rs13231897	0.82[ASN][1000 genomes]
rs17729097	0.82[ASN][1000 genomes]
rs2391175	0.82[ASN][1000 genomes]
rs35336240	0.82[ASN][1000 genomes]
rs4236321	0.82[ASN][1000 genomes]
rs4412274	0.82[ASN][1000 genomes]
rs4422683	0.82[ASN][1000 genomes]
rs4640955	0.82[ASN][1000 genomes]
rs4722545	0.82[ASN][1000 genomes]
rs4722546	0.82[ASN][1000 genomes]
rs4722547	0.82[ASN][1000 genomes]
rs4722548	0.82[ASN][1000 genomes]
rs66700050	0.82[ASN][1000 genomes]
rs67494041	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6977848	0.82[ASN][1000 genomes]
rs735316	0.82[ASN][1000 genomes]
rs7810017	0.82[ASN][1000 genomes]
rs997988	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv606432	chr7:25988185-26223294	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	esv3394736	chr7:25989527-25992275	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	90 gene(s)	inside rSNPs	diseases
5	esv3425784	chr7:25989652-25992200	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:25987200-25993200	Active TSS	Pancreas	Pancrea
2	chr7:25987800-25992800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr7:25989000-25991400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:25989200-25991400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr7:25989200-25991600	Active TSS	Rectal Smooth Muscle	rectum
6	chr7:25989200-25992600	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr7:25989400-25990600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr7:25989400-25990600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
9	chr7:25989400-25991400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:25989400-25991400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr7:25989400-25991400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr7:25989400-25991400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr7:25989400-25991400	Active TSS	Gastric	stomach
14	chr7:25989400-25991600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:25989400-25991600	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr7:25989400-25991600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr7:25989400-25991800	Active TSS	Fetal Kidney	kidney
18	chr7:25989400-25992000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:25989400-25992400	Active TSS	H9 Cell Line	embryonic stem cell
20	chr7:25989600-25990600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr7:25989600-25990600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr7:25989600-25990800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr7:25989600-25990800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
24	chr7:25989600-25991000	Active TSS	Right Atrium	heart
25	chr7:25989600-25991200	Active TSS	GM12878-XiMat	blood
26	chr7:25989600-25991400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr7:25989600-25991400	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr7:25989600-25991400	Active TSS	Esophagus	oesophagus
29	chr7:25989600-25991400	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr7:25989600-25991400	Bivalent/Poised TSS	NH-A	brain
31	chr7:25989600-25991600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr7:25989600-25991600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:25989600-25991800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr7:25989600-25991800	Active TSS	Ovary	ovary
35	chr7:25989600-25992000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr7:25989600-25992000	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr7:25989800-25990600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
38	chr7:25989800-25990800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr7:25989800-25991200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:25989800-25991200	Bivalent/Poised TSS	HSMMtube	muscle
41	chr7:25989800-25991400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:25989800-25991400	Active TSS	Aorta	Aorta
43	chr7:25989800-25991400	Active TSS	Psoas Muscle	Psoas
44	chr7:25989800-25991400	Active TSS	Small Intestine	intestine
45	chr7:25989800-25991600	Active TSS	Stomach Mucosa	stomach
46	chr7:25989800-25991600	Active TSS	Thymus	Thymus
47	chr7:25990000-25990600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
48	chr7:25990000-25990600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr7:25990000-25990600	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr7:25990000-25990800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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