Variant report

Variant	rs59976090
Chromosome Location	chr6:5458513-5458514
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	STAT3	chr6:5458231-5458923	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr6:5458099-5458653	T-47D	breast:	n/a	n/a
3	FOS	chr6:5458282-5458825	MCF10A-Er-Src	breast:	n/a	chr6:5458715-5458725 chr6:5458714-5458725 chr6:5458715-5458725 chr6:5458715-5458725 chr6:5458715-5458725 chr6:5458716-5458724
4	FOS	chr6:5458177-5458884	MCF10A-Er-Src	breast:	n/a	chr6:5458715-5458725 chr6:5458714-5458725 chr6:5458715-5458725 chr6:5458715-5458725 chr6:5458715-5458725 chr6:5458716-5458724
5	FOS	chr6:5457213-5458888	MCF10A-Er-Src	breast:	n/a	chr6:5458715-5458725 chr6:5458714-5458725 chr6:5457439-5457449 chr6:5458715-5458725 chr6:5458715-5458725 chr6:5457438-5457450 chr6:5457438-5457449 chr6:5458715-5458725 chr6:5457440-5457448 chr6:5457439-5457449 chr6:5458716-5458724
6	POLR2A	chr6:5457075-5459002	MCF10A-Er-Src	breast:	n/a	n/a
7	REST	chr6:5458442-5458755	PFSK-1	brain:	n/a	chr6:5458590-5458603 chr6:5458644-5458664 chr6:5458648-5458661
8	GATA3	chr6:5458060-5458568	T-47D	breast:	n/a	chr6:5458388-5458396 chr6:5458494-5458504
9	STAT3	chr6:5457211-5459125	MCF10A-Er-Src	breast:	n/a	chr6:5457590-5457598 chr6:5457319-5457331 chr6:5457946-5457953
10	FOS	chr6:5458223-5458964	MCF10A-Er-Src	breast:	n/a	chr6:5458715-5458725 chr6:5458714-5458725 chr6:5458715-5458725 chr6:5458715-5458725 chr6:5458715-5458725 chr6:5458716-5458724
11	GATA3	chr6:5458031-5458579	T-47D	breast:	n/a	chr6:5458388-5458396 chr6:5458494-5458504
12	FOXA1	chr6:5458044-5458618	T-47D	breast:	n/a	n/a
13	REST	chr6:5458400-5458810	SK-N-SH	brain:	n/a	chr6:5458590-5458603 chr6:5458644-5458664 chr6:5458648-5458661
14	POLR2A	chr6:5457251-5458629	MCF10A-Er-Src	breast:	n/a	n/a
15	MYC	chr6:5458077-5458940	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr6:5457181-5459118	MCF10A-Er-Src	breast:	n/a	chr6:5457590-5457598 chr6:5457319-5457331 chr6:5457946-5457953
17	MYC	chr6:5458086-5458738	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr6:5458201-5459166	MCF10A-Er-Src	breast:	n/a	n/a
19	STAT3	chr6:5457211-5459122	MCF10A-Er-Src	breast:	n/a	chr6:5457590-5457598 chr6:5457319-5457331 chr6:5457946-5457953

Variant related genes	Relation type
ENSG00000269985	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2020028	1.00[AMR][1000 genomes]
rs55951971	1.00[AMR][1000 genomes]
rs56670098	1.00[AMR][1000 genomes]
rs59218577	1.00[AMR][1000 genomes]
rs59668620	1.00[AMR][1000 genomes]
rs73352429	1.00[AMR][1000 genomes]
rs73352453	1.00[AMR][1000 genomes]
rs73352457	1.00[AMR][1000 genomes]
rs73718042	1.00[AMR][1000 genomes]
rs73718073	1.00[AMR][1000 genomes]
rs73718079	1.00[AMR][1000 genomes]
rs73718080	1.00[AMR][1000 genomes]
rs73718081	1.00[AMR][1000 genomes]
rs73718082	1.00[AMR][1000 genomes]
rs73718083	1.00[AMR][1000 genomes]
rs73718084	1.00[AMR][1000 genomes]
rs73718085	1.00[AMR][1000 genomes]
rs7745552	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv883418	chr6:5307432-5501389	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1034607	chr6:5311590-5573514	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv538120	chr6:5311590-5573514	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1023027	chr6:5377308-5556749	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv538121	chr6:5377308-5556749	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv600886	chr6:5426265-5511614	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1017506	chr6:5443538-5551125	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5433600-5461400	Weak transcription	Fetal Stomach	stomach
2	chr6:5434200-5487000	Weak transcription	Aorta	Aorta
3	chr6:5437400-5471200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:5438200-5471200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:5439600-5459800	Weak transcription	Primary T cells from cord blood	blood
6	chr6:5447600-5460600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:5448600-5466800	Weak transcription	Primary B cells from cord blood	blood
8	chr6:5449000-5499400	Weak transcription	Fetal Intestine Large	intestine
9	chr6:5450800-5459600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:5453000-5471000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr6:5453200-5460600	Weak transcription	Dnd41	blood
12	chr6:5454800-5472000	Weak transcription	Spleen	Spleen
13	chr6:5455000-5459000	Enhancers	Adipose Nuclei	Adipose
14	chr6:5455000-5460000	Enhancers	Fetal Brain Male	brain
15	chr6:5455800-5458600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:5456400-5486000	Weak transcription	Thymus	Thymus
17	chr6:5456600-5460200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:5456800-5458600	Enhancers	Brain Hippocampus Middle	brain
19	chr6:5456800-5458800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr6:5457000-5458600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:5457000-5458600	Enhancers	Right Atrium	heart
22	chr6:5457000-5458800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:5457000-5458800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:5457000-5458800	Enhancers	Brain Angular Gyrus	brain
25	chr6:5457000-5458800	Enhancers	Gastric	stomach
26	chr6:5457000-5459000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:5457000-5459000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:5457000-5459000	Enhancers	Brain Cingulate Gyrus	brain
29	chr6:5457000-5459000	Enhancers	HSMMtube	muscle
30	chr6:5457000-5459200	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr6:5457000-5459800	Enhancers	Osteobl	bone
32	chr6:5457000-5460000	Enhancers	HSMM	muscle
33	chr6:5457200-5459200	Enhancers	Brain Anterior Caudate	brain
34	chr6:5457400-5458800	Enhancers	Fetal Brain Female	brain
35	chr6:5457400-5481200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr6:5457600-5458600	Weak transcription	Right Ventricle	heart
37	chr6:5457600-5459200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr6:5457600-5459600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:5457600-5466400	Weak transcription	NHDF-Ad	bronchial
40	chr6:5457600-5472600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:5457800-5458600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:5457800-5460000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:5457800-5463200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:5457800-5471400	Weak transcription	Brain Substantia Nigra	brain
45	chr6:5457800-5487400	Weak transcription	Fetal Intestine Small	intestine
46	chr6:5458000-5458600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:5458000-5458600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:5458000-5458600	Enhancers	Left Ventricle	heart
49	chr6:5458200-5458600	Flanking Active TSS	HMEC	breast
50	chr6:5458200-5458800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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