Variant report

Variant	rs28392827
Chromosome Location	chr6:13486489-13486490
allele	A/C
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	SIN3AK20	chr6:13486195-13486786	K562	blood:	n/a	n/a
2	MXI1	chr6:13484535-13488686	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr6:13486048-13486651	GM12892	blood:	n/a	n/a
4	POLR2A	chr6:13485907-13488270	GM18951	blood:	n/a	n/a
5	POLR2A	chr6:13485921-13488226	GM12892	blood:	n/a	n/a
6	ELF1	chr6:13486206-13486791	K562	blood:	n/a	n/a
7	MAX	chr6:13486246-13487267	HUVEC	blood vessel:	n/a	chr6:13486482-13486492
8	CHD2	chr6:13486173-13486687	GM12878	blood:	n/a	n/a
9	ZNF143	chr6:13485857-13487179	GM12878	blood:	n/a	n/a
10	RCOR1	chr6:13486231-13486489	GM12878	blood:	n/a	n/a
11	MYC	chr6:13486067-13488139	NB4	blood:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
12	GATA3	chr6:13486397-13486741	T-47D	breast:	n/a	n/a
13	CHD1	chr6:13485653-13487078	GM12878	blood:	n/a	n/a
14	SIN3A	chr6:13485974-13487504	GM12878	blood:	n/a	chr6:13487441-13487454
15	MAX	chr6:13486184-13488812	GM12878	blood:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
16	SIN3AK20	chr6:13486204-13486766	SK-N-SH	brain:	n/a	n/a
17	MYC	chr6:13486170-13488139	K562	blood:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
18	POLR2A	chr6:13486331-13488405	H1-hESC	embryonic stem cell:	n/a	n/a
19	MYC	chr6:13486201-13486707	K562	blood:	n/a	chr6:13486482-13486492
20	MTA3	chr6:13486087-13486656	GM12878	blood:	n/a	n/a
21	MXI1	chr6:13486134-13487276	H1-hESC	embryonic stem cell:	n/a	n/a
22	SMC3	chr6:13485901-13488192	Hela-S3	cervix:	n/a	n/a
23	MAX	chr6:13486122-13489098	ECC-1	luminal epithelium:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
24	HCFC1	chr6:13486210-13486709	K562	blood:	n/a	n/a
25	MYC	chr6:13486169-13487984	K562	blood:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
26	MAX	chr6:13486152-13488018	Hela-S3	cervix:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
27	POLR2A	chr6:13486007-13486621	GM12892	blood:	n/a	n/a
28	MAX	chr6:13485823-13488217	K562	blood:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
29	CHD2	chr6:13486273-13486697	K562	blood:	n/a	n/a
30	MYC	chr6:13486048-13487263	MCF10A-Er-Src	breast:	n/a	chr6:13486482-13486492
31	GATA3	chr6:13486455-13486782	T-47D	breast:	n/a	n/a
32	MAX	chr6:13486151-13488394	HCT-116	colon:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
33	MAX	chr6:13486166-13487307	SK-N-SH	brain:	n/a	chr6:13486482-13486492
34	MAX	chr6:13486178-13489004	ECC-1	luminal epithelium:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
35	STAT1	chr6:13485831-13486670	GM12878	blood:	n/a	chr6:13486475-13486487
36	POLR2A	chr6:13485620-13486608	GM12878	blood:	n/a	n/a
37	MAX	chr6:13486136-13487354	MCF-7	breast:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
38	MAX	chr6:13486114-13488111	SK-N-SH	brain:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
39	SIN3A	chr6:13485845-13488935	H1-hESC	embryonic stem cell:	n/a	chr6:13487441-13487454 chr6:13487722-13487733
40	MAZ	chr6:13486207-13488199	Hela-S3	cervix:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
41	MAZ	chr6:13486205-13487304	GM12878	blood:	n/a	chr6:13486482-13486492
42	POLR2A	chr6:13485963-13488286	GM19193	blood:	n/a	n/a
43	BHLHE40	chr6:13485785-13487912	K562	blood:	n/a	chr6:13486336-13486352 chr6:13487437-13487453 chr6:13487232-13487248
44	UBTF	chr6:13486005-13488042	K562	blood:	n/a	n/a
45	E2F6	chr6:13486464-13489361	H1-hESC	embryonic stem cell:	n/a	chr6:13488882-13488892 chr6:13488624-13488633 chr6:13487750-13487760 chr6:13488144-13488158 chr6:13488515-13488524
46	TBP	chr6:13486212-13486670	K562	blood:	n/a	n/a
47	MAX	chr6:13486320-13487242	A549	lung:	n/a	chr6:13486482-13486492
48	TBP	chr6:13485872-13486514	GM12878	blood:	n/a	n/a
49	MAX	chr6:13486146-13486660	A549	lung:	n/a	chr6:13486482-13486492
50	POLR2A	chr6:13485896-13488307	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:13273285..13276286-chr6:13486162..13489029,3	K562	blood:
2	chr6:13273285..13276286-chr6:13486162..13489029,4	K562	blood:
3	chr6:13484664..13490672-chr6:13572714..13577234,9	K562	blood:
4	chr6:13484393..13490113-chr6:13572102..13578017,14	MCF-7	breast:
5	chr6:13465251..13472690-chr6:13481619..13489131,10	K562	blood:
6	chr6:13326316..13328538-chr6:13485562..13488530,2	MCF-7	breast:
7	chr6:13471062..13472931-chr6:13486374..13489089,2	MCF-7	breast:
8	chr6:13486147..13488786-chr6:13613803..13616517,3	K562	blood:
9	chr6:13485388..13489511-chr6:13572660..13577514,13	MCF-7	breast:
10	chr6:13325999..13330365-chr6:13484429..13488653,6	MCF-7	breast:
11	chr6:13406818..13408886-chr6:13483840..13488220,5	MCF-7	breast:
12	chr6:13484642..13487748-chr6:13572714..13576594,3	K562	blood:

Variant related genes	Relation type
ENSG00000187461	TF binding region
GFOD1-AS1	TF binding region
GFOD1	TF binding region
ENSG00000145979	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000261071	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000215022	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3421701	chr6:13485573-13489871	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer 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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13483200-13488800	Active TSS	Right Atrium	heart
2	chr6:13483400-13487600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:13484200-13488600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:13484600-13487200	Flanking Active TSS	Liver	Liver
5	chr6:13484600-13488400	Active TSS	GM12878-XiMat	blood
6	chr6:13484800-13487200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr6:13484800-13488400	Active TSS	Right Ventricle	heart
8	chr6:13485000-13486600	Active TSS	Colonic Mucosa	Colon
9	chr6:13485000-13488800	Active TSS	Brain Angular Gyrus	brain
10	chr6:13485000-13489600	Active TSS	Rectal Smooth Muscle	rectum
11	chr6:13485200-13488200	Active TSS	Stomach Smooth Muscle	stomach
12	chr6:13485200-13488200	Active TSS	NHLF	lung
13	chr6:13485200-13488600	Active TSS	Left Ventricle	heart
14	chr6:13485200-13488600	Active TSS	A549	lung
15	chr6:13485200-13488800	Active TSS	Brain Anterior Caudate	brain
16	chr6:13485200-13488800	Active TSS	Psoas Muscle	Psoas
17	chr6:13485400-13487200	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr6:13485400-13487200	Active TSS	Fetal Brain Male	brain
19	chr6:13485400-13487600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr6:13485400-13488600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:13485400-13488600	Active TSS	NHDF-Ad	bronchial
22	chr6:13485600-13486800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
23	chr6:13485600-13487000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
24	chr6:13485600-13488200	Active TSS	Placenta Amnion	Placenta Amnion
25	chr6:13485600-13488200	Active TSS	HSMMtube	muscle
26	chr6:13485600-13488600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr6:13485600-13488600	Active TSS	Esophagus	oesophagus
28	chr6:13485600-13488600	Active TSS	Lung	lung
29	chr6:13485600-13488800	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr6:13485600-13488800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr6:13485600-13489000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:13485800-13486600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:13485800-13486800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:13485800-13487000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
35	chr6:13485800-13487200	Flanking Active TSS	Placenta	Placenta
36	chr6:13485800-13487400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
37	chr6:13485800-13487400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr6:13485800-13488600	Active TSS	Ovary	ovary
39	chr6:13486000-13486600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:13486000-13486600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:13486000-13486800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:13486000-13486800	Active TSS	HepG2	liver
43	chr6:13486000-13487000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:13486000-13487000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:13486000-13487000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:13486000-13487200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:13486000-13487200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr6:13486000-13487400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr6:13486000-13487400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
50	chr6:13486000-13487600	Active TSS	Fetal Heart	heart

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