Variant report

Variant	rs560940239
Chromosome Location	chr5:179920684-179920685
allele	-/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	PBX3	chr5:179920578-179920690	GM12878	blood:	n/a	chr5:179920647-179920656
2	BATF	chr5:179920672-179920856	GM12878	blood:	n/a	n/a
3	GATA3	chr5:179920473-179920762	T-47D	breast:	n/a	n/a
4	HA-E2F1	chr5:179920670-179922511	MCF-7	breast:	n/a	chr5:179921995-179922005 chr5:179921246-179921255 chr5:179922003-179922012 chr5:179922199-179922206 chr5:179922199-179922206 chr5:179921250-179921260 chr5:179922199-179922206 chr5:179921998-179922008

No.	Distal block	Cell Line	Cell type
1	chr5:179920260..179922999-chr5:180038598..180040134,2	MCF-7	breast:
2	chr5:179720972..179723069-chr5:179918796..179921248,2	MCF-7	breast:
3	chr5:179920138..179923580-chr5:179954774..179958751,3	MCF-7	breast:
4	chr5:179778332..179781251-chr5:179920436..179923318,3	MCF-7	breast:
5	chr5:179919075..179921338-chr5:180210769..180213087,2	MCF-7	breast:
6	chr5:179718755..179721306-chr5:179919977..179922949,4	MCF-7	breast:

Variant related genes	Relation type
CNOT6	TF binding region
ENSG00000113300	Chromatin interaction
ENSG00000037280	Chromatin interaction
ENSG00000248367	Chromatin interaction
ENSG00000050748	Chromatin interaction
ENSG00000131459	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1019519	chr5:179866730-179959408	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv3356496	chr5:179920371-179922919	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179915000-179921000	Weak transcription	Aorta	Aorta
2	chr5:179917400-179920800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:179918400-179921000	Weak transcription	Lung	lung
4	chr5:179918600-179921000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:179918600-179921000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:179918800-179921600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:179919000-179920800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:179919000-179921000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:179919000-179921000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:179919400-179920800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr5:179919800-179920800	Enhancers	Fetal Thymus	thymus
12	chr5:179919800-179921400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:179920000-179920800	Enhancers	Primary B cells from peripheral blood	blood
14	chr5:179920000-179920800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr5:179920000-179920800	Flanking Active TSS	Dnd41	blood
16	chr5:179920000-179921200	Enhancers	Fetal Brain Male	brain
17	chr5:179920200-179920800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr5:179920200-179920800	Enhancers	Fetal Muscle Trunk	muscle
19	chr5:179920200-179920800	Enhancers	HMEC	breast
20	chr5:179920200-179921000	Enhancers	Primary B cells from cord blood	blood
21	chr5:179920200-179921000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:179920200-179921000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:179920200-179921000	Enhancers	Pancreas	Pancrea
24	chr5:179920200-179922200	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr5:179920400-179920800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:179920400-179920800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
27	chr5:179920400-179920800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:179920400-179920800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr5:179920400-179920800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr5:179920400-179920800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:179920400-179920800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr5:179920400-179920800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr5:179920400-179920800	Flanking Active TSS	Brain Hippocampus Middle	brain
34	chr5:179920400-179920800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr5:179920400-179920800	Enhancers	Fetal Lung	lung
36	chr5:179920400-179920800	Enhancers	Fetal Muscle Leg	muscle
37	chr5:179920400-179920800	Enhancers	Fetal Stomach	stomach
38	chr5:179920400-179920800	Flanking Active TSS	A549	lung
39	chr5:179920400-179920800	Flanking Active TSS	NHDF-Ad	bronchial
40	chr5:179920400-179920800	Enhancers	NHEK	skin
41	chr5:179920400-179921000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:179920400-179921000	Enhancers	Primary hematopoietic stem cells	blood
43	chr5:179920400-179921000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr5:179920400-179921000	Enhancers	Stomach Mucosa	stomach
45	chr5:179920400-179921200	Enhancers	Fetal Heart	heart
46	chr5:179920400-179921600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr5:179920400-179922200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:179920400-179922200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:179920400-179922200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:179920400-179922200	Active TSS	Brain Substantia Nigra	brain

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