Variant report

Variant	rs17166454
Chromosome Location	chr5:98274601-98274602
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	POLR2A	chr5:98271988-98274936	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr5:98274564-98275525	MCF10A-Er-Src	breast:	n/a	n/a
3	PBX3	chr5:98274038-98274688	SK-N-SH	brain:	n/a	n/a
4	FOXA1	chr5:98274134-98274614	HepG2	liver:	n/a	n/a
5	TCF12	chr5:98274123-98274744	SK-N-SH	brain:	n/a	chr5:98274363-98274373
6	TCF12	chr5:98274017-98274756	SK-N-SH	brain:	n/a	chr5:98274363-98274373
7	POLR2A	chr5:98274340-98275532	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98261788..98268544-chr5:98272174..98280784,17	MCF-7	breast:

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

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10044680	1.00[EUR][1000 genomes]
rs10045317	1.00[EUR][1000 genomes]
rs10046011	1.00[EUR][1000 genomes]
rs10060286	1.00[EUR][1000 genomes]
rs13358830	1.00[EUR][1000 genomes]
rs1382336	0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs161743	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162139	0.85[LWK][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs162141	0.88[LWK][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162142	1.00[EUR][1000 genomes]
rs162143	0.85[LWK][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs162157	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs162161	1.00[AMR][1000 genomes]
rs162162	0.91[ASW][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs170579	0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17166397	1.00[EUR][1000 genomes]
rs17166450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs179175	1.00[EUR][1000 genomes]
rs1828171	1.00[EUR][1000 genomes]
rs28782775	1.00[EUR][1000 genomes]
rs325196	1.00[AMR][1000 genomes]
rs325198	1.00[EUR][1000 genomes]
rs325210	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs325216	1.00[EUR][1000 genomes]
rs327801	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs327802	0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs327805	1.00[EUR][1000 genomes]
rs451883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57969582	1.00[EUR][1000 genomes]
rs59156696	1.00[EUR][1000 genomes]
rs61578983	1.00[EUR][1000 genomes]
rs6891520	1.00[EUR][1000 genomes]
rs73151499	1.00[EUR][1000 genomes]
rs73153514	1.00[EUR][1000 genomes]
rs73153532	1.00[EUR][1000 genomes]
rs73155421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73155423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7727696	0.82[YRI][hapmap];1.00[EUR][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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266000-98276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:98266000-98276400	Weak transcription	Placenta	Placenta
3	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
4	chr5:98266400-98276200	Weak transcription	Fetal Kidney	kidney
5	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
6	chr5:98266800-98277000	Weak transcription	HMEC	breast
7	chr5:98266800-98278400	Weak transcription	Hela-S3	cervix
8	chr5:98266800-98283200	Weak transcription	Duodenum Mucosa	Duodenum
9	chr5:98267400-98277800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:98270000-98275600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:98270200-98276400	Weak transcription	Fetal Thymus	thymus
12	chr5:98271000-98276000	Weak transcription	Primary T cells from cord blood	blood
13	chr5:98271200-98275000	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:98271600-98276200	Weak transcription	Primary B cells from cord blood	blood
15	chr5:98272200-98276600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:98272200-98277600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:98272400-98275000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr5:98272400-98275200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr5:98272400-98276200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:98272400-98276600	Enhancers	K562	blood
21	chr5:98272400-98278000	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr5:98272600-98275000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr5:98272600-98275000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr5:98272600-98275000	Enhancers	Osteobl	bone
25	chr5:98272600-98275200	Enhancers	Fetal Heart	heart
26	chr5:98272600-98275600	Enhancers	Fetal Muscle Leg	muscle
27	chr5:98272600-98277200	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr5:98272600-98278600	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr5:98272800-98274800	Enhancers	Psoas Muscle	Psoas
30	chr5:98272800-98277400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:98273000-98274800	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr5:98273000-98274800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr5:98273000-98275600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr5:98273200-98274800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:98273200-98274800	Enhancers	HepG2	liver
36	chr5:98273400-98274800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:98273400-98275200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:98273400-98275200	Enhancers	NHDF-Ad	bronchial
39	chr5:98273400-98276200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:98273600-98274800	Enhancers	H9 Cell Line	embryonic stem cell
41	chr5:98273600-98274800	Flanking Active TSS	HSMMtube	muscle
42	chr5:98273600-98275000	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr5:98273600-98275000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr5:98273600-98277800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr5:98273800-98274800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr5:98273800-98275000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:98273800-98275400	Enhancers	Brain Substantia Nigra	brain
48	chr5:98273800-98276200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr5:98274000-98274800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:98274000-98274800	Enhancers	Brain Inferior Temporal Lobe	brain

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