Variant report

Variant	rs549391663
Chromosome Location	chr6:56954755-56954756
allele	G/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	TCF7L2	chr6:56954592-56955101	Hela-S3	cervix:	n/a	chr6:56954887-56954901 chr6:56954890-56954897
2	SIN3AK20	chr6:56954551-56955097	PFSK-1	brain:	n/a	n/a
3	MAZ	chr6:56954550-56955075	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:56954584-56954774	A549	lung:	n/a	n/a
5	POLR2A	chr6:56954539-56955371	A549	lung:	n/a	n/a
6	USF2	chr6:56954469-56954998	GM12878	blood:	n/a	chr6:56954714-56954730
7	ETS1	chr6:56954544-56954996	GM12878	blood:	n/a	chr6:56954792-56954805 chr6:56954791-56954804
8	POLR2A	chr6:56954647-56955535	MCF-7	breast:	n/a	n/a
9	ETS1	chr6:56954546-56955074	GM12878	blood:	n/a	chr6:56954792-56954805 chr6:56954791-56954804
10	GABPA	chr6:56954590-56955305	HepG2	liver:	n/a	n/a
11	POLR2A	chr6:56954436-56955204	HEK293	kidney:	n/a	n/a
12	TCF7L2	chr6:56954583-56955094	MCF-7	breast:	n/a	chr6:56954887-56954901 chr6:56954890-56954897
13	STAT5A	chr6:56954465-56955072	GM12878	blood:	n/a	n/a
14	GATA3	chr6:56954651-56955037	T-47D	breast:	n/a	chr6:56954751-56954761
15	SP1	chr6:56954397-56955086	HCT-116	colon:	n/a	chr6:56954712-56954722 chr6:56954712-56954722 chr6:56954711-56954722 chr6:56954711-56954723
16	SRF	chr6:56954645-56954898	GM12878	blood:	n/a	n/a
17	NFATC1	chr6:56954440-56955097	GM12878	blood:	n/a	n/a
18	SIN3AK20	chr6:56954499-56955118	H1-hESC	embryonic stem cell:	n/a	n/a
19	ETS1	chr6:56954492-56955164	K562	blood:	n/a	chr6:56954792-56954805 chr6:56954791-56954804
20	BCLAF1	chr6:56954456-56955077	GM12878	blood:	n/a	n/a
21	ZC3H11A	chr6:56954439-56954919	K562	blood:	n/a	n/a
22	POLR2A	chr6:56954384-56955093	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr6:56954541-56955109	HCT-116	colon:	n/a	n/a
24	POLR2A	chr6:56954538-56955827	H1-hESC	embryonic stem cell:	n/a	n/a
25	MYC	chr6:56954333-56955142	K562	blood:	n/a	n/a
26	POLR2A	chr6:56954546-56955759	Hela-S3	cervix:	n/a	n/a
27	TBP	chr6:56954510-56955074	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr6:56954494-56955199	NB4	blood:	n/a	n/a
29	E2F6	chr6:56954549-56955071	H1-hESC	embryonic stem cell:	n/a	chr6:56954972-56954983
30	TCF12	chr6:56954479-56955110	ECC-1	luminal epithelium:	n/a	chr6:56954725-56954732 chr6:56954694-56954701 chr6:56954693-56954703 chr6:56954504-56954513
31	POLR2A	chr6:56954629-56955193	MCF10A-Er-Src	breast:	n/a	n/a
32	RCOR1	chr6:56954543-56954970	GM12878	blood:	n/a	n/a
33	REST	chr6:56954543-56955465	SK-N-SH	brain:	n/a	chr6:56954712-56954725
34	POLR2A	chr6:56954637-56955471	MCF-7	breast:	n/a	n/a
35	CTCF	chr6:56954720-56954870	RPTEC	kidney:	n/a	n/a
36	SIN3AK20	chr6:56954576-56955601	HepG2	liver:	n/a	n/a
37	CTCF	chr6:56954496-56954993	K562	blood:	n/a	n/a
38	USF2	chr6:56954535-56954833	HepG2	liver:	n/a	chr6:56954714-56954730
39	RCOR1	chr6:56954363-56955123	K562	blood:	n/a	n/a
40	SIN3AK20	chr6:56954529-56955131	K562	blood:	n/a	n/a
41	TAF1	chr6:56954499-56955073	H1-neurons	neurons:	n/a	n/a
42	NR2F2	chr6:56954064-56955216	K562	blood:	n/a	chr6:56954199-56954214
43	GABPA	chr6:56954257-56955129	MCF-7	breast:	n/a	n/a
44	GABPA	chr6:56954637-56955252	GM12878	blood:	n/a	n/a
45	ETS1	chr6:56954548-56955114	K562	blood:	n/a	chr6:56954792-56954805 chr6:56954791-56954804
46	NFIC	chr6:56954406-56955094	HepG2	liver:	n/a	n/a
47	YY1	chr6:56954540-56955146	K562	blood:	n/a	n/a
48	IRF1	chr6:56954445-56955077	K562	blood:	n/a	chr6:56954523-56954533 chr6:56954709-56954723 chr6:56954523-56954537 chr6:56954522-56954539 chr6:56954522-56954534 chr6:56954538-56954548 chr6:56954519-56954533
49	PML	chr6:56954546-56955058	GM12878	blood:	n/a	chr6:56954843-56954851
50	FOXA1	chr6:56954643-56955006	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:56954167..56956467-chr6:57034197..57037095,2	K562	blood:
2	chr6:56818718..56821144-chr6:56954189..56956169,2	MCF-7	breast:
3	chr6:56954591..56956568-chr6:57036921..57038610,2	MCF-7	breast:
4	chr6:56818533..56822842-chr6:56954657..56959004,6	K562	blood:
5	chr6:56911241..56911877-chr6:56954515..56955089,3	Hela-S3	cervix:

Variant related genes	Relation type
ZNF451	TF binding region
ENSG00000151917	Chromatin interaction
ENSG00000226803	Chromatin interaction
ENSG00000112208	Chromatin interaction
ENSG00000168116	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv970717	chr6:56903957-56955783	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	esv3374787	chr6:56912959-56955113	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer 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	8 gene(s)	inside rSNPs	diseases
9	nsv350038	chr6:56953752-56960124	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 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	chr6:56927000-56954800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:56935200-56954800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:56953200-56954800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:56954000-56966800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:56954200-56954800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:56954200-56954800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr6:56954200-56954800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:56954200-56954800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr6:56954200-56954800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr6:56954200-56954800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:56954200-56954800	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr6:56954200-56954800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:56954200-56954800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr6:56954200-56954800	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr6:56954200-56954800	Flanking Active TSS	Dnd41	blood
16	chr6:56954200-56954800	Flanking Active TSS	HUVEC	blood vessel
17	chr6:56954200-56954800	Flanking Active TSS	NHEK	skin
18	chr6:56954200-56954800	Flanking Active TSS	Osteobl	bone
19	chr6:56954200-56955000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:56954200-56955000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:56954200-56955200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:56954200-56955200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:56954200-56955200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:56954200-56955200	Active TSS	Brain Angular Gyrus	brain
25	chr6:56954200-56955200	Active TSS	Brain Anterior Caudate	brain
26	chr6:56954200-56955200	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr6:56954200-56955200	Active TSS	Fetal Kidney	kidney
28	chr6:56954200-56955200	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr6:56954200-56955200	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr6:56954200-56955200	Active TSS	A549	lung
31	chr6:56954400-56954800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:56954400-56954800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:56954400-56954800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr6:56954400-56954800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr6:56954400-56954800	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr6:56954400-56954800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr6:56954400-56954800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr6:56954400-56954800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr6:56954400-56954800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
40	chr6:56954400-56954800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
41	chr6:56954400-56954800	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr6:56954400-56954800	Flanking Active TSS	Liver	Liver
43	chr6:56954400-56954800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr6:56954400-56954800	Active TSS	Fetal Brain Male	brain
45	chr6:56954400-56954800	Flanking Active TSS	Fetal Intestine Large	intestine
46	chr6:56954400-56954800	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr6:56954400-56954800	Flanking Active TSS	NH-A	brain
48	chr6:56954400-56955200	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr6:56954400-56955200	Active TSS	H9 Cell Line	embryonic stem cell
50	chr6:56954400-56955200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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