Variant report

Variant	rs10153497
Chromosome Location	chr19:38897246-38897247
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	chr19:38897228-38897501	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38891109..38897587-chr19:38900077..38906045,7	MCF-7	breast:

Variant related genes	Relation type
FAM98C	TF binding region
ENSG00000171777	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11880285	1.00[AMR][1000 genomes]
rs11881714	1.00[AMR][1000 genomes]
rs2286548	1.00[AMR][1000 genomes]
rs2302185	1.00[AMR][1000 genomes]
rs45589333	1.00[AMR][1000 genomes]
rs57249964	1.00[AMR][1000 genomes]
rs57347571	1.00[AMR][1000 genomes]
rs57361474	1.00[AMR][1000 genomes]
rs58247981	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58490212	1.00[AMR][1000 genomes]
rs58591078	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59047386	1.00[AMR][1000 genomes]
rs59776537	1.00[AMR][1000 genomes]
rs59845491	1.00[AMR][1000 genomes]
rs60068553	1.00[AMR][1000 genomes]
rs60491875	1.00[AMR][1000 genomes]
rs61648033	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv1055309	chr19:38896244-38945851	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38894400-38898600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:38894400-38898800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr19:38894400-38903400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:38894400-38908000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:38894600-38897400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:38894600-38897400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr19:38894600-38898000	Weak transcription	Psoas Muscle	Psoas
8	chr19:38894600-38898600	Weak transcription	Fetal Kidney	kidney
9	chr19:38894600-38899200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:38894600-38900400	Weak transcription	A549	lung
11	chr19:38894600-38900400	Weak transcription	NHDF-Ad	bronchial
12	chr19:38894600-38900400	Weak transcription	NHLF	lung
13	chr19:38894600-38900600	Weak transcription	NH-A	brain
14	chr19:38894600-38902000	Weak transcription	HSMM	muscle
15	chr19:38894600-38902000	Weak transcription	NHEK	skin
16	chr19:38894600-38907800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:38894600-38908000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:38894600-38908400	Weak transcription	Left Ventricle	heart
19	chr19:38894600-38908400	Weak transcription	HUVEC	blood vessel
20	chr19:38894800-38897400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:38894800-38900000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:38894800-38900600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:38894800-38902400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:38894800-38908000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:38894800-38908400	Weak transcription	Small Intestine	intestine
26	chr19:38895000-38897400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr19:38895000-38897400	Weak transcription	Fetal Brain Female	brain
28	chr19:38895000-38901000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:38895000-38901000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:38895000-38903400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:38895000-38905800	Weak transcription	Brain Germinal Matrix	brain
32	chr19:38895000-38907800	Weak transcription	GM12878-XiMat	blood
33	chr19:38895000-38908000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr19:38895000-38908400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr19:38895200-38897400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr19:38895200-38898200	Weak transcription	Stomach Mucosa	stomach
37	chr19:38895200-38900000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr19:38895200-38904200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:38895200-38906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr19:38895200-38907800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:38895200-38908200	Weak transcription	Fetal Thymus	thymus
42	chr19:38895400-38897400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr19:38895400-38897400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr19:38895400-38897800	Strong transcription	Esophagus	oesophagus
45	chr19:38895400-38898000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:38895400-38898000	Strong transcription	Brain Hippocampus Middle	brain
47	chr19:38895400-38898000	Strong transcription	Colon Smooth Muscle	Colon
48	chr19:38895400-38898200	Strong transcription	Fetal Muscle Leg	muscle
49	chr19:38895400-38900000	Strong transcription	Fetal Intestine Small	intestine
50	chr19:38895400-38900000	Strong transcription	Fetal Stomach	stomach

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