Variant report

Variant	rs6879839
Chromosome Location	chr5:98277354-98277355
allele	C/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	TBL1XR1	chr5:98277320-98277436	K562	blood:	n/a	n/a
2	FOS	chr5:98277160-98277495	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr5:98277238-98277509	MCF10A-Er-Src	breast:	n/a	n/a
4	CEBPB	chr5:98277283-98277477	K562	blood:	n/a	chr5:98277331-98277342
5	FOS	chr5:98277012-98277476	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr5:98277003-98278079	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr5:98277185-98277402	MCF10A-Er-Src	breast:	n/a	n/a
8	MYC	chr5:98276996-98277495	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr5:98277187-98277495	MCF10A-Er-Src	breast:	n/a	n/a
10	STAT3	chr5:98277191-98277391	MCF10A-Er-Src	breast:	n/a	n/a
11	CEBPB	chr5:98277325-98277358	HepG2	liver:	n/a	chr5:98277331-98277342
12	POLR2A	chr5:98275181-98279858	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr5:98277186-98277443	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr5:98277041-98277434	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:98272097..98275128-chr5:98275593..98280478,6	MCF-7	breast:
2	chr5:98276533..98278644-chr5:98288923..98290589,2	K562	blood:
3	chr5:98269604..98273895-chr5:98275576..98277950,6	K562	blood:
4	chr5:98275762..98278033-chr5:98288005..98290423,2	K562	blood:
5	chr5:98276177..98277799-chr5:98286832..98289590,2	MCF-7	breast:
6	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200351	TF binding region
ENSG00000200351	Chromatin interaction
ENSG00000248489	Chromatin interaction
ENSG00000241597	Chromatin interaction
ENSG00000153922	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs58665823	1.00[AMR][1000 genomes]
rs6873625	1.00[AMR][1000 genomes]
rs7702910	1.00[AMR][1000 genomes]
rs7724992	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537818	chr5:98241627-98279192	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
2	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
3	chr5:98266800-98278400	Weak transcription	Hela-S3	cervix
4	chr5:98266800-98283200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:98267400-98277800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:98272200-98277600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:98272400-98278000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr5:98272600-98278600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr5:98272800-98277400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr5:98273600-98277800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr5:98274600-98280000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr5:98274800-98277400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:98274800-98278800	Weak transcription	HepG2	liver
14	chr5:98274800-98282800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:98274800-98297200	Weak transcription	Thymus	Thymus
16	chr5:98275800-98277400	Enhancers	Brain Substantia Nigra	brain
17	chr5:98275800-98277600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr5:98275800-98277800	Enhancers	Colon Smooth Muscle	Colon
19	chr5:98276000-98278000	Enhancers	Fetal Muscle Leg	muscle
20	chr5:98276000-98278600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr5:98276200-98277400	Enhancers	Brain Angular Gyrus	brain
22	chr5:98276200-98277400	Enhancers	Brain Hippocampus Middle	brain
23	chr5:98276200-98277400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr5:98276200-98277600	Enhancers	Stomach Smooth Muscle	stomach
25	chr5:98276200-98278200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:98276200-98278800	Enhancers	Primary B cells from cord blood	blood
27	chr5:98276200-98281600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:98276400-98277400	Enhancers	Ovary	ovary
29	chr5:98276400-98277600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr5:98276400-98277600	Enhancers	Left Ventricle	heart
31	chr5:98276400-98277600	Enhancers	Rectal Smooth Muscle	rectum
32	chr5:98276400-98277600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr5:98276400-98277800	Enhancers	Placenta	Placenta
34	chr5:98276400-98277800	Enhancers	Right Atrium	heart
35	chr5:98276400-98278200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr5:98276600-98277400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:98276600-98277400	Weak transcription	K562	blood
38	chr5:98276600-98277600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:98276600-98282800	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:98276800-98277400	Enhancers	Brain Cingulate Gyrus	brain
41	chr5:98276800-98278000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr5:98277000-98277600	Enhancers	HMEC	breast
43	chr5:98277000-98277800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr5:98277000-98278800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr5:98277000-98279200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:98277200-98277600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:98277200-98277800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr5:98277200-98278400	Weak transcription	Fetal Lung	lung
49	chr5:98277200-98280000	Weak transcription	Psoas Muscle	Psoas
50	chr5:98277200-98281200	Weak transcription	Right Ventricle	heart

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