Variant report

Variant	rs561485742
Chromosome Location	chr6:33398253-33398254
allele	A/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	RELA	chr6:33398109-33398898	GM19193	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
2	CEBPB	chr6:33398238-33398500	HepG2	liver:	n/a	n/a
3	RUNX3	chr6:33397922-33398515	GM12878	blood:	n/a	n/a
4	EBF1	chr6:33398208-33398485	GM12878	blood:	n/a	chr6:33398371-33398382
5	RELA	chr6:33398068-33398938	GM18505	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
6	RELA	chr6:33398007-33399061	GM18951	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
7	RELA	chr6:33398026-33398970	GM10847	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
8	CEBPB	chr6:33398215-33398511	IMR90	lung:	n/a	n/a
9	POLR2A	chr6:33398042-33399915	SK-N-MC	brain:	n/a	n/a
10	RELA	chr6:33397963-33399236	GM19099	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
11	BHLHE40	chr6:33398029-33398578	GM12878	blood:	n/a	n/a
12	HNF4A	chr6:33398201-33398524	HepG2	liver:	n/a	chr6:33398386-33398401 chr6:33398393-33398401
13	CEBPB	chr6:33398187-33398562	HepG2	liver:	n/a	n/a
14	MAZ	chr6:33398235-33399507	IMR90	lung:	n/a	chr6:33399285-33399295 chr6:33399302-33399309 chr6:33399420-33399430 chr6:33399300-33399311
15	CEBPB	chr6:33398244-33398537	K562	blood:	n/a	n/a
16	RELA	chr6:33398098-33399128	GM15510	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
17	RUNX3	chr6:33397977-33398504	GM12878	blood:	n/a	n/a
18	CEBPB	chr6:33398207-33398564	HepG2	liver:	n/a	n/a
19	HNF4A	chr6:33398200-33398535	HepG2	liver:	n/a	chr6:33398386-33398401 chr6:33398393-33398401
20	EBF1	chr6:33398158-33398915	GM12878	blood:	n/a	chr6:33398371-33398382
21	FOXA1	chr6:33398096-33398582	HepG2	liver:	n/a	n/a
22	RELA	chr6:33397899-33398943	GM12878	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
23	POLR2A	chr6:33398112-33400875	H1-hESC	embryonic stem cell:	n/a	n/a
24	RELA	chr6:33398015-33399018	GM12891	blood:	n/a	chr6:33398299-33398308 chr6:33398299-33398308
25	STAT5A	chr6:33397956-33398425	GM12878	blood:	n/a	chr6:33398140-33398152
26	NFIC	chr6:33398000-33398435	GM12878	blood:	n/a	n/a
27	MTA3	chr6:33397969-33399774	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:33279489..33293095-chr6:33375317..33398824,56	K562	blood:
2	chr6:33263619..33269524-chr6:33392449..33400505,13	K562	blood:
3	chr6:33283041..33291527-chr6:33390658..33398493,18	K562	blood:
4	chr6:33395899..33401993-chr6:33420102..33423796,11	MCF-7	breast:
5	chr6:33238168..33246812-chr6:33390354..33398427,26	K562	blood:
6	chr6:33395342..33398838-chr6:33677022..33679442,4	K562	blood:
7	chr6:33358270..33361160-chr6:33397889..33401606,4	K562	blood:
8	chr6:33173944..33176266-chr6:33397713..33400457,2	K562	blood:
9	chr6:33392449..33400629-chr6:33419013..33424035,12	MCF-7	breast:
10	chr6:33237732..33247113-chr6:33390735..33401356,31	K562	blood:
11	chr6:33254824..33258515-chr6:33394130..33398725,7	K562	blood:
12	chr6:33396539..33398732-chr6:33463165..33465539,2	K562	blood:
13	chr6:33394932..33398976-chr6:33412593..33416199,4	MCF-7	breast:
14	chr6:33357884..33361160-chr6:33397889..33401606,5	K562	blood:

Variant related genes	Relation type
SYNGAP1	TF binding region
ENSG00000237441	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000236104	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000199036	Chromatin interaction
ENSG00000204209	Chromatin interaction
ENSG00000204220	Chromatin interaction
ENSG00000231500	Chromatin interaction
ENSG00000223501	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000213588	Chromatin interaction
ENSG00000227057	Chromatin interaction
ENSG00000235863	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	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
2	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv885769	chr6:33377522-33412197	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv932196	chr6:33383131-33400706	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
6	nsv1019212	chr6:33398031-33413930	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33396000-33401400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:33396200-33399200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:33396200-33399800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr6:33396200-33400000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr6:33396200-33400000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr6:33396200-33400200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr6:33396200-33400200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr6:33396200-33400400	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr6:33396200-33400400	Flanking Active TSS	GM12878-XiMat	blood
10	chr6:33396400-33398800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:33396400-33398800	Enhancers	Brain Substantia Nigra	brain
12	chr6:33396400-33398800	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr6:33396400-33399000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:33396400-33399000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:33396400-33399200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:33396400-33401200	Enhancers	Spleen	Spleen
17	chr6:33396400-33401600	Enhancers	Fetal Heart	heart
18	chr6:33396400-33403000	Weak transcription	Ovary	ovary
19	chr6:33396400-33405200	Weak transcription	Psoas Muscle	Psoas
20	chr6:33396600-33398400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:33396600-33398400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:33396600-33398600	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:33396600-33398600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr6:33396600-33398600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr6:33396600-33398600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr6:33396600-33398600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr6:33396600-33398600	Enhancers	Adipose Nuclei	Adipose
28	chr6:33396600-33398600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr6:33396600-33398600	Enhancers	HepG2	liver
30	chr6:33396600-33398800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:33396600-33398800	Enhancers	Primary B cells from peripheral blood	blood
32	chr6:33396600-33399000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:33396600-33399000	Enhancers	Colon Smooth Muscle	Colon
34	chr6:33396600-33399200	Enhancers	Fetal Intestine Small	intestine
35	chr6:33396600-33399200	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr6:33396600-33399400	Enhancers	HMEC	breast
37	chr6:33396600-33399600	Enhancers	Liver	Liver
38	chr6:33396600-33399600	Enhancers	Fetal Intestine Large	intestine
39	chr6:33396600-33399600	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr6:33396600-33400600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr6:33396600-33400600	Enhancers	Fetal Muscle Leg	muscle
42	chr6:33396600-33400600	Enhancers	Lung	lung
43	chr6:33396600-33400800	Weak transcription	Right Atrium	heart
44	chr6:33396600-33401000	Weak transcription	HSMMtube	muscle
45	chr6:33396600-33416000	Weak transcription	Pancreas	Pancrea
46	chr6:33396800-33398600	Enhancers	H9 Cell Line	embryonic stem cell
47	chr6:33396800-33398600	Enhancers	Primary B cells from cord blood	blood
48	chr6:33396800-33398600	Enhancers	Fetal Thymus	thymus
49	chr6:33396800-33398600	Weak transcription	Rectal Smooth Muscle	rectum
50	chr6:33396800-33398600	Enhancers	A549	lung

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