Variant report

Variant	rs139836825
Chromosome Location	chr9:2621366-2621367
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	RUNX3	chr9:2621152-2621448	GM12878	blood:	n/a	n/a
3	CTCF	chr9:2621340-2621490	GM12866	blood:	n/a	n/a
4	CEBPB	chr9:2621194-2621559	MCF-7	breast:	n/a	n/a
5	MAZ	chr9:2621194-2621464	GM12878	blood:	n/a	n/a
6	CTCF	chr9:2621260-2621410	AG09309	skin:	n/a	n/a
7	MAX	chr9:2621135-2621972	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr9:2621360-2621510	HMEC	breast:	n/a	n/a
9	POLR2A	chr9:2620945-2622528	U87	brain:	n/a	n/a
10	POLR2A	chr9:2621166-2621982	A549	lung:	n/a	n/a
11	POLR2A	chr9:2621269-2622611	Hela-S3	cervix:	n/a	n/a
12	RAD21	chr9:2621285-2621506	HepG2	liver:	n/a	n/a
13	CTCF	chr9:2621300-2621450	AG04450	lung:	n/a	n/a
14	RCOR1	chr9:2621133-2621653	K562	blood:	n/a	n/a
15	NFYB	chr9:2621290-2621678	GM12878	blood:	n/a	n/a
16	USF1	chr9:2621315-2621711	SK-N-SH_RA	brain:	n/a	chr9:2621658-2621674 chr9:2621583-2621599
17	ZNF143	chr9:2621165-2621578	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr9:2621144-2622705	MCF-7	breast:	n/a	n/a
19	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
20	CTCF	chr9:2621340-2621490	HMF	breast:	n/a	n/a
21	RFX5	chr9:2621338-2621401	GM12878	blood:	n/a	n/a
22	CHD2	chr9:2621351-2621538	GM12878	blood:	n/a	n/a
23	REST	chr9:2620800-2623973	H1-neurons	neurons:	n/a	chr9:2621948-2621961 chr9:2622878-2622891 chr9:2621769-2621787 chr9:2621771-2621784 chr9:2622822-2622842
24	POLR2A	chr9:2621022-2622340	HL-60	blood:	n/a	n/a
25	MAX	chr9:2621185-2621953	NB4	blood:	n/a	n/a
26	POLR2A	chr9:2621192-2621727	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr9:2621320-2621470	HCPEpiC	choroid plexus:	n/a	n/a
28	ELF1	chr9:2621268-2621522	HepG2	liver:	n/a	chr9:2621437-2621449
29	RUNX3	chr9:2621218-2621695	GM12878	blood:	n/a	n/a
30	POLR2A	chr9:2621169-2621604	SK-N-SH	brain:	n/a	n/a
31	CREB1	chr9:2621228-2621757	A549	lung:	n/a	n/a
32	GTF2F1	chr9:2621278-2621595	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr9:2621150-2621901	MCF-7	breast:	n/a	n/a
34	POLR2A	chr9:2621076-2621984	H1-hESC	embryonic stem cell:	n/a	n/a
35	CTCF	chr9:2621314-2621496	MCF-7	breast:	n/a	n/a
36	TBP	chr9:2620958-2621701	H1-hESC	embryonic stem cell:	n/a	n/a
37	CEBPB	chr9:2621303-2621449	HepG2	liver:	n/a	n/a
38	JUND	chr9:2621310-2621515	K562	blood:	n/a	n/a
39	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
40	CTCF	chr9:2621296-2621498	NHEK	skin:	n/a	n/a
41	CTCF	chr9:2621300-2621450	AG09319	gingival:	n/a	n/a
42	CTCF	chr9:2621340-2621490	HRPEpiC	eye:	n/a	n/a
43	MAX	chr9:2621144-2621986	HepG2	liver:	n/a	n/a
44	CTCF	chr9:2621360-2621510	HRE	kidney:	n/a	n/a
45	CHD1	chr9:2620886-2622127	IMR90	lung:	n/a	n/a
46	MAX	chr9:2620942-2624127	A549	lung:	n/a	chr9:2623485-2623494 chr9:2623484-2623495 chr9:2623484-2623495 chr9:2623668-2623678
47	TAF7	chr9:2621121-2621633	H1-hESC	embryonic stem cell:	n/a	n/a
48	CTCF	chr9:2621360-2621510	WERI-Rb-1	eye:	n/a	n/a
49	CTCF	chr9:2621331-2621477	GM12891	blood:	n/a	n/a
50	CEBPB	chr9:2621171-2621587	HepG2	liver:	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
2	lnc-KIAA0020-1	chr9:2621229-2621413	ENSG00000236404.4
3	lnc-KIAA0020-1	chr9:2621229-2621413	ENSG00000236404

Variant related genes	Relation type
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:122 , 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	chr9:2620200-2621400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:2620200-2621400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
6	chr9:2620200-2623600	Active TSS	Brain Anterior Caudate	brain
7	chr9:2620400-2621400	Flanking Active TSS	Dnd41	blood
8	chr9:2620400-2622200	Active TSS	Fetal Brain Female	brain
9	chr9:2620400-2623200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr9:2620400-2623800	Active TSS	H9 Cell Line	embryonic stem cell
11	chr9:2620600-2621400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:2620600-2621400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
13	chr9:2620600-2621400	Flanking Active TSS	Brain Germinal Matrix	brain
14	chr9:2620600-2621400	Flanking Active TSS	Fetal Brain Male	brain
15	chr9:2620600-2621600	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr9:2620600-2622400	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr9:2620600-2624000	Active TSS	Right Atrium	heart
18	chr9:2620600-2624200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr9:2620800-2621400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr9:2620800-2621400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr9:2620800-2621400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:2620800-2621400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr9:2620800-2621400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr9:2620800-2621400	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr9:2620800-2621400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr9:2620800-2621600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:2620800-2622000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:2620800-2623600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:2620800-2623600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr9:2620800-2623800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:2620800-2623800	Active TSS	Brain Angular Gyrus	brain
32	chr9:2620800-2623800	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr9:2620800-2623800	Active TSS	A549	lung
34	chr9:2620800-2624000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:2620800-2624000	Active TSS	Fetal Kidney	kidney
36	chr9:2620800-2624400	Active TSS	Right Ventricle	heart
37	chr9:2621000-2621400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr9:2621000-2621400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:2621000-2621400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:2621000-2621400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
41	chr9:2621000-2621400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
42	chr9:2621000-2621400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
43	chr9:2621000-2621400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr9:2621000-2621400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
45	chr9:2621000-2621400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
46	chr9:2621000-2621400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:2621000-2621400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr9:2621000-2621400	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr9:2621000-2621400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
50	chr9:2621000-2621400	Active TSS	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links