Variant report

Variant	rs17166461
Chromosome Location	chr5:98278990-98278991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98272097..98275128-chr5:98275593..98280478,6	MCF-7	breast:
2	chr5:98263406..98266421-chr5:98277549..98281338,5	MCF-7	breast:
3	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200351	Chromatin interaction
ENSG00000248489	Chromatin interaction
ENSG00000153922	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1007453	1.00[ASW][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs10515285	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17166367	0.89[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs17166368	0.89[LWK][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap]
rs17166471	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17166564	0.89[AFR][1000 genomes]
rs35394679	1.00[ASW][hapmap];0.94[LWK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs3860806	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55654090	0.89[AFR][1000 genomes]
rs55660533	0.84[AFR][1000 genomes]
rs57249217	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57253975	0.86[AFR][1000 genomes]
rs58477983	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60298381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61515191	0.86[AFR][1000 genomes]
rs6864720	1.00[ASW][hapmap];0.94[LWK][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes]
rs6890688	0.86[YRI][hapmap]
rs6895731	0.89[LWK][hapmap];0.83[MKK][hapmap];0.86[YRI][hapmap]
rs731496	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73153574	0.88[AFR][1000 genomes]
rs73153600	0.98[AFR][1000 genomes]
rs73155410	0.89[AFR][1000 genomes]
rs73155434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73155446	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73155478	0.86[AFR][1000 genomes]
rs73155484	0.81[AFR][1000 genomes]
rs73157407	0.89[AFR][1000 genomes]
rs73157426	0.93[AFR][1000 genomes]
rs73776061	0.83[AFR][1000 genomes]
rs7707061	1.00[ASW][hapmap];0.95[LWK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs7726385	0.81[AFR][1000 genomes]
rs7727349	0.83[LWK][hapmap]
rs7732611	0.89[AFR][1000 genomes]
rs963689	0.86[AFR][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:40 , 50 per page) page: 1

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	chr5:98266800-98283200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:98274600-98280000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr5:98274800-98282800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:98274800-98297200	Weak transcription	Thymus	Thymus
7	chr5:98276200-98281600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:98276600-98282800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:98277000-98279200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:98277200-98280000	Weak transcription	Psoas Muscle	Psoas
11	chr5:98277200-98281200	Weak transcription	Right Ventricle	heart
12	chr5:98277200-98282000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:98277200-98283000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr5:98277400-98279000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:98277400-98281600	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:98277400-98282000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:98277400-98282000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:98277400-98282200	Weak transcription	Brain Substantia Nigra	brain
19	chr5:98277600-98281400	Weak transcription	Left Ventricle	heart
20	chr5:98277600-98281800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:98277600-98283000	Weak transcription	HMEC	breast
22	chr5:98277800-98279000	Weak transcription	Placenta	Placenta
23	chr5:98277800-98279400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr5:98277800-98280200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:98277800-98281000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr5:98277800-98281400	Weak transcription	Right Atrium	heart
27	chr5:98278000-98279200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr5:98278000-98279800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:98278400-98279200	Enhancers	Fetal Muscle Leg	muscle
30	chr5:98278400-98279200	Enhancers	Hela-S3	cervix
31	chr5:98278400-98279400	Enhancers	Fetal Lung	lung
32	chr5:98278400-98280000	Enhancers	K562	blood
33	chr5:98278600-98279000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr5:98278600-98299400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:98278800-98279000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:98278800-98279000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:98278800-98279200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr5:98278800-98279200	Enhancers	HepG2	liver
39	chr5:98278800-98279400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr5:98278800-98281600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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