Variant report

Variant	rs6939203
Chromosome Location	chr6:4778505-4778506
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	chr6:4777462-4778900	GM12878	blood:	n/a	n/a
2	RELA	chr6:4777389-4778895	GM18951	blood:	n/a	n/a
3	ATF2	chr6:4778161-4778898	GM12878	blood:	n/a	n/a
4	FOS	chr6:4778457-4778587	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr6:4778345-4778851	GM12878	blood:	n/a	chr6:4778684-4778695
6	CEBPB	chr6:4778412-4778776	A549	lung:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
7	RCOR1	chr6:4778325-4778807	GM12878	blood:	n/a	n/a
8	EP300	chr6:4778345-4778703	GM12878	blood:	n/a	n/a
9	YY1	chr6:4778207-4778566	GM12878	blood:	n/a	n/a
10	STAT5A	chr6:4778064-4778852	GM12878	blood:	n/a	chr6:4778684-4778695
11	POLR2A	chr6:4777394-4778648	GM12891	blood:	n/a	n/a
12	CREB1	chr6:4778167-4778918	GM12878	blood:	n/a	n/a
13	RFX5	chr6:4778340-4778674	GM12878	blood:	n/a	n/a
14	CUX1	chr6:4778432-4779173	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:4777261-4778617	GM12891	blood:	n/a	n/a
16	CBX3	chr6:4778271-4778844	HCT-116	colon:	n/a	n/a
17	POLR2A	chr6:4777385-4778548	GM12878	blood:	n/a	n/a
18	NFATC1	chr6:4778028-4779019	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:4777962-4778574	GM12892	blood:	n/a	n/a
20	FOXM1	chr6:4778155-4778867	GM12878	blood:	n/a	n/a
21	ATF2	chr6:4778124-4778824	GM12878	blood:	n/a	n/a
22	CBX3	chr6:4778104-4778750	K562	blood:	n/a	n/a
23	SETDB1	chr6:4778111-4778964	U2OS	brain:	n/a	n/a
24	NFIC	chr6:4778165-4778686	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:4778157-4778509	GM12891	blood:	n/a	n/a
26	TBL1XR1	chr6:4778142-4778972	GM12878	blood:	n/a	n/a
27	BHLHE40	chr6:4777336-4778808	GM12878	blood:	n/a	n/a
28	KAP1	chr6:4777817-4779068	K562	blood:	n/a	n/a
29	KAP1	chr6:4777767-4778872	HEK293	kidney:	n/a	n/a
30	CEBPB	chr6:4778393-4778711	HepG2	liver:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
31	FOS	chr6:4778373-4778683	MCF10A-Er-Src	breast:	n/a	n/a
32	MTA3	chr6:4778058-4778837	GM12878	blood:	n/a	n/a
33	BCLAF1	chr6:4778228-4778689	GM12878	blood:	n/a	n/a
34	CEBPB	chr6:4778367-4778722	K562	blood:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
35	CBX3	chr6:4778236-4778740	K562	blood:	n/a	n/a
36	PML	chr6:4778009-4778800	GM12878	blood:	n/a	n/a
37	EBF1	chr6:4778134-4778757	GM12878	blood:	n/a	n/a
38	CEBPB	chr6:4778331-4778751	Hela-S3	cervix:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
39	CEBPB	chr6:4778387-4778689	IMR90	lung:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
40	CREB1	chr6:4778225-4778813	GM12878	blood:	n/a	n/a
41	TBP	chr6:4777392-4779043	GM12878	blood:	n/a	n/a
42	CEBPB	chr6:4777403-4778870	GM12878	blood:	n/a	chr6:4778531-4778542 chr6:4778533-4778544
43	YY1	chr6:4778293-4778519	GM12891	blood:	n/a	n/a
44	EP300	chr6:4778186-4778765	GM12878	blood:	n/a	n/a
45	MTA3	chr6:4778155-4778738	GM12878	blood:	n/a	n/a
46	RELA	chr6:4777413-4778869	GM19193	blood:	n/a	n/a
47	IKZF1	chr6:4778253-4778896	GM12878	blood:	n/a	n/a
48	EP300	chr6:4778379-4778669	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr6:4777148-4778610	GM12892	blood:	n/a	n/a
50	ZNF143	chr6:4778029-4778970	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:4775417..4779410-chr6:4834974..4837006,3	MCF-7	breast:
2	chr6:4773447..4776687-chr6:4777915..4782551,4	MCF-7	breast:
3	chr6:4776139..4778956-chr6:5002447..5004557,2	K562	blood:
4	chr6:4488845..4492110-chr6:4777740..4781440,3	MCF-7	breast:
5	chr6:4775727..4780301-chr6:4925378..4930668,5	K562	blood:
6	chr6:4778081..4781516-chr6:4787216..4791667,5	MCF-7	breast:
7	chr6:4777710..4780092-chr6:4801744..4804702,2	K562	blood:

Variant related genes	Relation type
ENSG00000236336	TF binding region
ENSG00000260239	Chromatin interaction
ENSG00000236336	Chromatin interaction
ENSG00000124787	Chromatin interaction
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1265337	0.85[ASN][1000 genomes]
rs17346907	1.00[CHB][hapmap]
rs233480	1.00[CHB][hapmap]
rs4615435	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59124798	0.82[ASN][1000 genomes]
rs60530811	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61392817	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928581	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929349	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6939607	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs760791	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7746532	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7746925	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3366530	chr6:4471528-4865322	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv3429586	chr6:4719363-4792438	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	esv3445880	chr6:4775978-4778526	Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4775600-4778600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:4775800-4778800	Active TSS	GM12878-XiMat	blood
3	chr6:4775800-4778800	Active TSS	NHLF	lung
4	chr6:4777400-4778600	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr6:4777400-4778600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:4777400-4778600	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr6:4777600-4778600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
8	chr6:4777600-4778600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr6:4777600-4778600	Flanking Active TSS	Fetal Lung	lung
10	chr6:4777600-4778600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr6:4777800-4778600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:4777800-4778600	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr6:4777800-4780200	Weak transcription	Gastric	stomach
14	chr6:4777800-4783600	Weak transcription	Lung	lung
15	chr6:4777800-4789000	Weak transcription	Pancreas	Pancrea
16	chr6:4778000-4778600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr6:4778000-4778600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:4778000-4778600	Flanking Active TSS	Hela-S3	cervix
19	chr6:4778000-4778600	Transcr. at gene 5' and 3'	K562	blood
20	chr6:4778000-4779800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:4778000-4780400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:4778000-4782400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:4778200-4778600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:4778200-4778600	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr6:4778200-4778600	Active TSS	Rectal Smooth Muscle	rectum
26	chr6:4778200-4778600	Active TSS	HSMMtube	muscle
27	chr6:4778200-4778800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:4778200-4778800	ZNF genes & repeats	NHDF-Ad	bronchial
29	chr6:4778200-4779400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:4778200-4780000	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr6:4778200-4780000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr6:4778200-4780200	Enhancers	Primary B cells from peripheral blood	blood
33	chr6:4778200-4780200	Weak transcription	Ovary	ovary
34	chr6:4778200-4781000	Weak transcription	Osteobl	bone
35	chr6:4778200-4781400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:4778200-4781600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:4778200-4785000	Weak transcription	Psoas Muscle	Psoas
38	chr6:4778200-4787000	Weak transcription	Thymus	Thymus
39	chr6:4778400-4778600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:4778400-4778600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr6:4778400-4778600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:4778400-4778600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr6:4778400-4778600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr6:4778400-4778600	Enhancers	Primary hematopoietic stem cells	blood
45	chr6:4778400-4778600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:4778400-4778600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:4778400-4778600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:4778400-4778600	Enhancers	Brain Hippocampus Middle	brain
49	chr6:4778400-4778600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:4778400-4778600	Enhancers	Pancreatic Islets	Pancreatic Islet

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