Variant report

Variant	rs17780854
Chromosome Location	chr5:100190501-100190502
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:100187668..100190190-chr5:100190255..100193150,3	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10478648	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17160818	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17719528	0.83[AMR][1000 genomes]
rs17720901	1.00[AMR][1000 genomes]
rs17721341	1.00[AMR][1000 genomes]
rs17721790	1.00[AMR][1000 genomes]
rs17722713	1.00[AMR][1000 genomes]
rs17722756	0.85[AMR][1000 genomes]
rs17723146	1.00[AMR][1000 genomes]
rs17725086	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17725882	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17726376	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17775827	0.83[AMR][1000 genomes]
rs17775983	0.83[AMR][1000 genomes]
rs17776515	0.83[AMR][1000 genomes]
rs17777079	0.92[AMR][1000 genomes]
rs17777349	1.00[AMR][1000 genomes]
rs17778120	1.00[AMR][1000 genomes]
rs17778217	1.00[AMR][1000 genomes]
rs17778313	1.00[AMR][1000 genomes]
rs17778440	1.00[AMR][1000 genomes]
rs17778487	1.00[AMR][1000 genomes]
rs17778598	1.00[AMR][1000 genomes]
rs17778786	1.00[AMR][1000 genomes]
rs17779305	1.00[AMR][1000 genomes]
rs17779694	1.00[AMR][1000 genomes]
rs17779731	1.00[AMR][1000 genomes]
rs17780072	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17780121	1.00[AMR][1000 genomes]
rs17780992	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17781289	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17782650	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57652761	0.83[AMR][1000 genomes]
rs6866516	1.00[AMR][1000 genomes]
rs73777435	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73777437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	esv1834675	chr5:100143084-100535029	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 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	chr5:100147600-100218000	Weak transcription	Thymus	Thymus
2	chr5:100174000-100190600	Weak transcription	Fetal Lung	lung
3	chr5:100177600-100215400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:100178200-100218400	Weak transcription	Placenta	Placenta
5	chr5:100187000-100199200	Weak transcription	Lung	lung
6	chr5:100187200-100192800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:100187400-100190600	Enhancers	Primary hematopoietic stem cells	blood
8	chr5:100187800-100190800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr5:100187800-100191000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr5:100187800-100192400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:100187800-100193000	Enhancers	Primary B cells from peripheral blood	blood
12	chr5:100188200-100190800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr5:100188200-100191400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr5:100188200-100192200	Weak transcription	Spleen	Spleen
15	chr5:100188200-100192800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr5:100188400-100191000	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr5:100188400-100192200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:100188400-100192200	Weak transcription	Brain Germinal Matrix	brain
19	chr5:100188400-100194600	Strong transcription	Dnd41	blood
20	chr5:100188600-100191600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr5:100188800-100191800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:100189000-100191000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:100189000-100191600	Weak transcription	Fetal Brain Female	brain
24	chr5:100189200-100190800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr5:100189200-100190800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:100189200-100191000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr5:100189200-100193200	Weak transcription	Fetal Kidney	kidney
28	chr5:100189400-100190600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:100189600-100190600	Enhancers	Primary B cells from cord blood	blood
30	chr5:100189600-100190600	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr5:100189600-100191200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr5:100189800-100191000	Genic enhancers	Monocytes-CD14+_RO01746	blood
33	chr5:100190000-100190600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:100190000-100194200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:100190400-100190600	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr5:100190400-100190800	Flanking Active TSS	HUVEC	blood vessel
37	chr5:100190400-100191400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr5:100190400-100192200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr5:100190400-100192200	Strong transcription	Fetal Thymus	thymus
40	chr5:100190400-100192200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood

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