Variant report

Variant	rs546080769
Chromosome Location	chr9:2621490-2621491
allele	C/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	CTCF	chr9:2621360-2621510	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr9:2621340-2621490	GM12866	blood:	n/a	n/a
3	CEBPB	chr9:2621194-2621559	MCF-7	breast:	n/a	n/a
4	MAX	chr9:2621135-2621972	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr9:2621360-2621510	HMEC	breast:	n/a	n/a
6	POLR2A	chr9:2620945-2622528	U87	brain:	n/a	n/a
7	POLR2A	chr9:2621166-2621982	A549	lung:	n/a	n/a
8	POLR2A	chr9:2621269-2622611	Hela-S3	cervix:	n/a	n/a
9	RAD21	chr9:2621285-2621506	HepG2	liver:	n/a	n/a
10	RCOR1	chr9:2621133-2621653	K562	blood:	n/a	n/a
11	NFYB	chr9:2621290-2621678	GM12878	blood:	n/a	n/a
12	USF1	chr9:2621315-2621711	SK-N-SH_RA	brain:	n/a	chr9:2621658-2621674 chr9:2621583-2621599
13	ZNF143	chr9:2621165-2621578	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr9:2621144-2622705	MCF-7	breast:	n/a	n/a
15	YY1	chr9:2621273-2621709	HepG2	liver:	n/a	chr9:2621576-2621596 chr9:2621647-2621661 chr9:2621590-2621604 chr9:2621589-2621603 chr9:2621589-2621598 chr9:2621583-2621597
16	CTCF	chr9:2621340-2621490	HMF	breast:	n/a	n/a
17	CHD2	chr9:2621351-2621538	GM12878	blood:	n/a	n/a
18	REST	chr9:2620800-2623973	H1-neurons	neurons:	n/a	chr9:2621948-2621961 chr9:2622878-2622891 chr9:2621769-2621787 chr9:2621771-2621784 chr9:2622822-2622842
19	POLR2A	chr9:2621022-2622340	HL-60	blood:	n/a	n/a
20	MAX	chr9:2621185-2621953	NB4	blood:	n/a	n/a
21	POLR2A	chr9:2621192-2621727	H1-hESC	embryonic stem cell:	n/a	n/a
22	ELF1	chr9:2621268-2621522	HepG2	liver:	n/a	chr9:2621437-2621449
23	RUNX3	chr9:2621218-2621695	GM12878	blood:	n/a	n/a
24	POLR2A	chr9:2621169-2621604	SK-N-SH	brain:	n/a	n/a
25	CREB1	chr9:2621228-2621757	A549	lung:	n/a	n/a
26	GTF2F1	chr9:2621278-2621595	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr9:2621150-2621901	MCF-7	breast:	n/a	n/a
28	POLR2A	chr9:2621076-2621984	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr9:2621314-2621496	MCF-7	breast:	n/a	n/a
30	TBP	chr9:2620958-2621701	H1-hESC	embryonic stem cell:	n/a	n/a
31	JUND	chr9:2621310-2621515	K562	blood:	n/a	n/a
32	E2F6	chr9:2621134-2622057	A549	lung:	n/a	chr9:2621498-2621507 chr9:2621800-2621810 chr9:2621590-2621600 chr9:2621694-2621705 chr9:2621593-2621603 chr9:2621722-2621733 chr9:2621440-2621450
33	CTCF	chr9:2621296-2621498	NHEK	skin:	n/a	n/a
34	CTCF	chr9:2621340-2621490	HRPEpiC	eye:	n/a	n/a
35	MAX	chr9:2621144-2621986	HepG2	liver:	n/a	n/a
36	CTCF	chr9:2621360-2621510	HRE	kidney:	n/a	n/a
37	CHD1	chr9:2620886-2622127	IMR90	lung:	n/a	n/a
38	MAX	chr9:2620942-2624127	A549	lung:	n/a	chr9:2623485-2623494 chr9:2623484-2623495 chr9:2623484-2623495 chr9:2623668-2623678
39	TAF7	chr9:2621121-2621633	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr9:2621360-2621510	WERI-Rb-1	eye:	n/a	n/a
41	CEBPB	chr9:2621171-2621587	HepG2	liver:	n/a	n/a
42	CTCF	chr9:2621256-2621579	GM12878	blood:	n/a	n/a
43	CTCF	chr9:2621360-2621510	BJ	skin:	n/a	n/a
44	MAX	chr9:2621212-2621768	HepG2	liver:	n/a	n/a
45	RAD21	chr9:2621058-2621646	SK-N-SH_RA	brain:	n/a	n/a
46	CTCF	chr9:2621338-2621490	LNCaP	prostate:	n/a	n/a
47	USF1	chr9:2621334-2621652	SK-N-SH_RA	brain:	n/a	chr9:2621583-2621599
48	TBP	chr9:2621333-2621522	HepG2	liver:	n/a	n/a
49	CTCF	chr9:2621340-2621490	AoAF	blood vessel:	n/a	n/a
50	POLR2A	chr9:2621264-2621872	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2620987..2624573-chr9:2639977..2643677,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA0020-1	chr9:2619998-2621792	NONHSAT130002

Variant related genes	Relation type
ENSG00000236404	TF binding region
VLDLR	TF binding region
ENSG00000236404	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv1029876	chr9:2526760-2633562	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv892069	chr9:2600836-2631738	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv892070	chr9:2610307-2633921	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv892071	chr9:2618969-2626031	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv892072	chr9:2619915-2623253	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv824819	chr9:2620547-2623694	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv892073	chr9:2620592-2627365	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv527298	chr9:2621030-2631092	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2619800-2624000	Active TSS	Ovary	ovary
2	chr9:2620000-2624000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr9:2620000-2624200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:2620200-2623600	Active TSS	Brain Anterior Caudate	brain
5	chr9:2620400-2622200	Active TSS	Fetal Brain Female	brain
6	chr9:2620400-2623200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr9:2620400-2623800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr9:2620600-2621600	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr9:2620600-2622400	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr9:2620600-2624000	Active TSS	Right Atrium	heart
11	chr9:2620600-2624200	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr9:2620800-2621600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr9:2620800-2622000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr9:2620800-2623600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:2620800-2623600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:2620800-2623800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:2620800-2623800	Active TSS	Brain Angular Gyrus	brain
18	chr9:2620800-2623800	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr9:2620800-2623800	Active TSS	A549	lung
20	chr9:2620800-2624000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:2620800-2624000	Active TSS	Fetal Kidney	kidney
22	chr9:2620800-2624400	Active TSS	Right Ventricle	heart
23	chr9:2621000-2621600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:2621000-2621600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:2621000-2621600	Active TSS	Colonic Mucosa	Colon
26	chr9:2621000-2621600	Flanking Bivalent TSS/Enh	HepG2	liver
27	chr9:2621000-2622000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
28	chr9:2621000-2622400	Active TSS	H1 Cell Line	embryonic stem cell
29	chr9:2621000-2622400	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr9:2621000-2622400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:2621000-2622400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:2621000-2622400	Active TSS	GM12878-XiMat	blood
33	chr9:2621000-2623000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:2621000-2623000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:2621000-2623000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
36	chr9:2621000-2623000	Active TSS	Rectal Smooth Muscle	rectum
37	chr9:2621000-2623000	Active TSS	HSMMtube	muscle
38	chr9:2621000-2623600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:2621000-2623800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr9:2621000-2623800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:2621000-2623800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
42	chr9:2621000-2623800	Active TSS	Psoas Muscle	Psoas
43	chr9:2621000-2623800	Active TSS	NHLF	lung
44	chr9:2621000-2624000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
45	chr9:2621000-2624000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:2621000-2624200	Active TSS	Aorta	Aorta
47	chr9:2621000-2624200	Active TSS	Left Ventricle	heart
48	chr9:2621200-2621600	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr9:2621200-2621600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr9:2621200-2621600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood

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