Variant report

Variant	rs13374159
Chromosome Location	chr1:147142457-147142458
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	CTCF	chr1:147142340-147142490	Caco-2	colon:	n/a	n/a
2	POLR2A	chr1:147142304-147143001	HCT-116	colon:	n/a	n/a
3	SP1	chr1:147142448-147142943	HepG2	liver:	n/a	n/a
4	CTCF	chr1:147142400-147142550	AG04449	skin:	n/a	n/a
5	POLR2A	chr1:147141802-147142995	A549	lung:	n/a	n/a
6	MAX	chr1:147141463-147143213	HepG2	liver:	n/a	n/a
7	KAP1	chr1:147141501-147143108	HEK293	kidney:	n/a	n/a
8	POLR2A	chr1:147141502-147143032	HCT-116	colon:	n/a	n/a
9	WRNIP1	chr1:147142160-147142917	GM12878	blood:	n/a	n/a
10	SP1	chr1:147142178-147143059	A549	lung:	n/a	n/a
11	MAX	chr1:147141455-147143066	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr1:147142375-147143013	MCF10A-Er-Src	breast:	n/a	n/a
13	TBP	chr1:147142261-147142769	H1-hESC	embryonic stem cell:	n/a	n/a
14	TAF1	chr1:147142080-147143045	A549	lung:	n/a	n/a
15	POLR2A	chr1:147142206-147142976	GM12878	blood:	n/a	n/a
16	SIN3AK20	chr1:147142189-147143142	PANC-1	pancreas:	n/a	n/a
17	SMARCC1	chr1:147141561-147142954	Hela-S3	cervix:	n/a	chr1:147142718-147142727
18	POLR2A	chr1:147141584-147143018	GM18505	blood:	n/a	n/a
19	POLR2A	chr1:147142342-147143011	SK-N-MC	brain:	n/a	n/a
20	ZEB1	chr1:147142379-147142869	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:147141523-147143053	ECC-1	luminal epithelium:	n/a	n/a
22	ZBTB7A	chr1:147141902-147142949	ECC-1	luminal epithelium:	n/a	n/a
23	MYBL2	chr1:147142098-147143067	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:147141995-147142984	Gliobla	brain:	n/a	n/a
25	POLR2A	chr1:147142451-147142978	HepG2	liver:	n/a	n/a
26	POLR2A	chr1:147141574-147143101	MCF-7	breast:	n/a	n/a
27	MAZ	chr1:147141531-147143010	Hela-S3	cervix:	n/a	n/a
28	SMC3	chr1:147141512-147143011	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr1:147142337-147142960	MCF10A-Er-Src	breast:	n/a	n/a
30	BHLHE40	chr1:147142418-147142954	K562	blood:	n/a	n/a
31	MAFK	chr1:147141302-147143067	Hela-S3	cervix:	n/a	chr1:147141620-147141635 chr1:147142972-147142987
32	GATA3	chr1:147141242-147143000	MCF-7	breast:	n/a	chr1:147142456-147142465 chr1:147142456-147142463 chr1:147142452-147142468 chr1:147142455-147142465
33	MAX	chr1:147141358-147143173	MCF-7	breast:	n/a	n/a
34	POLR2A	chr1:147142303-147143011	Hela-S3	cervix:	n/a	n/a
35	STAT1	chr1:147142295-147142956	GM12878	blood:	n/a	n/a
36	ELF1	chr1:147141573-147143085	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:147141704-147143079	A549	lung:	n/a	n/a
38	YY1	chr1:147142431-147142914	SK-N-SH_RA	brain:	n/a	chr1:147142734-147142748
39	EP300	chr1:147142365-147142686	GM12878	blood:	n/a	chr1:147142650-147142666
40	MTA3	chr1:147141808-147142876	GM12878	blood:	n/a	n/a
41	CREB1	chr1:147142422-147142976	H1-hESC	embryonic stem cell:	n/a	n/a
42	SIX5	chr1:147142417-147142917	GM12878	blood:	n/a	chr1:147142718-147142727 chr1:147142720-147142729 chr1:147142716-147142730
43	ELF1	chr1:147141412-147143132	MCF-7	breast:	n/a	n/a
44	TAF1	chr1:147142427-147142782	H1-hESC	embryonic stem cell:	n/a	n/a
45	USF2	chr1:147142321-147142975	GM12878	blood:	n/a	n/a
46	SIX5	chr1:147142341-147143000	GM12878	blood:	n/a	chr1:147142718-147142727 chr1:147142720-147142729 chr1:147142716-147142730
47	TBP	chr1:147142211-147142792	HepG2	liver:	n/a	n/a
48	JUND	chr1:147142374-147142853	A549	lung:	n/a	chr1:147142771-147142780
49	PML	chr1:147141480-147143174	MCF-7	breast:	n/a	n/a
50	NFIC	chr1:147142297-147142698	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:147010483..147014086-chr1:147140786..147143809,3	MCF-7	breast:
2	chr1:147117692..147123079-chr1:147140177..147144336,6	MCF-7	breast:
3	chr1:147125294..147131165-chr1:147136519..147143336,11	MCF-7	breast:
4	chr1:146714651..146716663-chr1:147141111..147143150,2	MCF-7	breast:

Variant related genes	Relation type
ACP6	TF binding region
ENSG00000162836	Chromatin interaction
ENSG00000116128	Chromatin interaction
ENSG00000131781	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10465883	1.00[EUR][1000 genomes]
rs3766506	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs3766507	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs56936807	1.00[EUR][1000 genomes]
rs57463094	1.00[EUR][1000 genomes]
rs6672939	0.87[AFR][1000 genomes]
rs6673124	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6682543	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs946905	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs946907	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
3	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
7	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
9	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
15	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
16	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv534063	chr1:146807433-147381411	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
19	nsv1001868	chr1:146893791-147389944	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	27 gene(s)	inside rSNPs	diseases
20	nsv872266	chr1:147020099-147381558	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
21	nsv831426	chr1:147089930-147265267	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:147140800-147143200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:147141000-147143200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:147141000-147143200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:147141000-147143400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:147141200-147143000	Active TSS	Brain Hippocampus Middle	brain
6	chr1:147141200-147143200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr1:147141200-147143200	Active TSS	H1 Cell Line	embryonic stem cell
8	chr1:147141200-147143200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:147141200-147143200	Active TSS	Brain Angular Gyrus	brain
10	chr1:147141200-147143200	Active TSS	Fetal Intestine Large	intestine
11	chr1:147141200-147143200	Active TSS	Fetal Kidney	kidney
12	chr1:147141200-147143200	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:147141200-147143200	Active TSS	Psoas Muscle	Psoas
14	chr1:147141200-147143200	Active TSS	Right Atrium	heart
15	chr1:147141400-147142600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:147141400-147142800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:147141400-147142800	Active TSS	Pancreas	Pancrea
18	chr1:147141400-147143000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:147141400-147143000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:147141400-147143000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:147141400-147143000	Active TSS	Aorta	Aorta
22	chr1:147141400-147143000	Active TSS	Gastric	stomach
23	chr1:147141400-147143000	Active TSS	Left Ventricle	heart
24	chr1:147141400-147143000	Active TSS	Ovary	ovary
25	chr1:147141400-147143000	Active TSS	HSMMtube	muscle
26	chr1:147141400-147143000	Active TSS	NHDF-Ad	bronchial
27	chr1:147141400-147143200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:147141400-147143200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:147141400-147143200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:147141400-147143200	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr1:147141400-147143200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:147141400-147143200	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr1:147141400-147143200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr1:147141400-147143200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:147141400-147143200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:147141400-147143200	Active TSS	Fetal Stomach	stomach
37	chr1:147141400-147143200	Active TSS	Right Ventricle	heart
38	chr1:147141400-147143200	Active TSS	NHLF	lung
39	chr1:147141400-147143800	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr1:147141600-147142800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:147141600-147142800	Active TSS	Primary T cells from cord blood	blood
42	chr1:147141600-147142800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr1:147141600-147142800	Active TSS	Muscle Satellite Cultured Cells	--
44	chr1:147141600-147142800	Active TSS	Colonic Mucosa	Colon
45	chr1:147141600-147142800	Active TSS	Duodenum Mucosa	Duodenum
46	chr1:147141600-147142800	Active TSS	Fetal Lung	lung
47	chr1:147141600-147142800	Active TSS	K562	blood
48	chr1:147141600-147143000	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr1:147141600-147143000	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr1:147141600-147143000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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