Variant report

Variant	rs1654346
Chromosome Location	chr19:38550574-38550575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38549096..38551828-chr19:38559673..38561442,2	MCF-7	breast:
2	chr19:38395738..38398220-chr19:38547451..38552123,4	MCF-7	breast:
3	chr19:38543891..38548790-chr19:38549215..38554298,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000221258	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1630393	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654351	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654353	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1725471	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803708	0.88[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs855635	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1060359	chr19:38512719-38552438	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1062518	chr19:38540454-38564913	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38522000-38553600	Weak transcription	Stomach Smooth Muscle	stomach
2	chr19:38527800-38551800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
4	chr19:38531400-38550800	Weak transcription	NHLF	lung
5	chr19:38538400-38552800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
7	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
8	chr19:38540400-38551600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr19:38543400-38553600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:38543800-38563200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr19:38545800-38550800	Weak transcription	Osteobl	bone
12	chr19:38545800-38553600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr19:38546200-38551800	Weak transcription	HSMMtube	muscle
14	chr19:38546400-38553600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:38546600-38553600	Weak transcription	Brain Substantia Nigra	brain
16	chr19:38546600-38554000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:38547000-38551600	Weak transcription	NH-A	brain
19	chr19:38547000-38553400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr19:38547000-38553600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:38547000-38554800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:38547000-38563600	Weak transcription	Fetal Lung	lung
23	chr19:38547200-38550800	Weak transcription	Fetal Kidney	kidney
24	chr19:38547200-38561400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr19:38547600-38553200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:38548400-38551000	Enhancers	Primary B cells from peripheral blood	blood
27	chr19:38548600-38551400	Enhancers	Primary B cells from cord blood	blood
28	chr19:38548600-38551400	Enhancers	Fetal Thymus	thymus
29	chr19:38548600-38551400	Enhancers	GM12878-XiMat	blood
30	chr19:38548600-38554400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:38548600-38555000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:38548800-38550600	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr19:38548800-38551200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr19:38549000-38553000	Weak transcription	Brain Angular Gyrus	brain
35	chr19:38549000-38553000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr19:38549000-38553200	Weak transcription	Fetal Stomach	stomach
37	chr19:38549000-38553600	Weak transcription	Brain Hippocampus Middle	brain
38	chr19:38549200-38550800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr19:38549200-38551200	Enhancers	Primary hematopoietic stem cells	blood
40	chr19:38549200-38551600	Weak transcription	NHDF-Ad	bronchial
41	chr19:38549200-38551600	Weak transcription	NHEK	skin
42	chr19:38549200-38551800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:38549200-38551800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:38549200-38552000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:38549200-38552600	Weak transcription	Lung	lung
46	chr19:38549200-38552800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:38549200-38553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:38549200-38553400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr19:38549200-38564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr19:38549200-38572000	Weak transcription	Liver	Liver

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