Variant report

Variant	rs59491640
Chromosome Location	chr19:38897502-38897503
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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
ENSG00000171777	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11083454	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11538289	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2302228	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28384479	0.85[ASN][1000 genomes]
rs3745955	0.80[EUR][1000 genomes]
rs3745958	0.81[AFR][1000 genomes]
rs3745959	0.85[AFR][1000 genomes]
rs3745963	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57753437	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60780508	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508791	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6508792	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6508793	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245668	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246085	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246191	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246213	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248540	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248780	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257976	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043029	0.81[EUR][1000 genomes]
rs73043030	0.93[EUR][1000 genomes]
rs73043033	0.93[EUR][1000 genomes]
rs73043098	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73044905	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044911	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044915	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044917	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044919	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044923	0.80[EUR][1000 genomes]
rs73044926	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044928	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044930	1.00[EUR][1000 genomes]
rs73044932	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044937	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044942	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044944	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044946	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73044947	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73044948	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044953	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8108440	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109713	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8112499	0.85[AMR][1000 genomes];1.00[EUR][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:114 , 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	chr19:38894600-38898000	Weak transcription	Psoas Muscle	Psoas
6	chr19:38894600-38898600	Weak transcription	Fetal Kidney	kidney
7	chr19:38894600-38899200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:38894600-38900400	Weak transcription	A549	lung
9	chr19:38894600-38900400	Weak transcription	NHDF-Ad	bronchial
10	chr19:38894600-38900400	Weak transcription	NHLF	lung
11	chr19:38894600-38900600	Weak transcription	NH-A	brain
12	chr19:38894600-38902000	Weak transcription	HSMM	muscle
13	chr19:38894600-38902000	Weak transcription	NHEK	skin
14	chr19:38894600-38907800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:38894600-38908000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:38894600-38908400	Weak transcription	Left Ventricle	heart
17	chr19:38894600-38908400	Weak transcription	HUVEC	blood vessel
18	chr19:38894800-38900000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:38894800-38900600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:38894800-38902400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:38894800-38908000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:38894800-38908400	Weak transcription	Small Intestine	intestine
23	chr19:38895000-38901000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:38895000-38901000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:38895000-38903400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:38895000-38905800	Weak transcription	Brain Germinal Matrix	brain
27	chr19:38895000-38907800	Weak transcription	GM12878-XiMat	blood
28	chr19:38895000-38908000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr19:38895000-38908400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:38895200-38898200	Weak transcription	Stomach Mucosa	stomach
31	chr19:38895200-38900000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr19:38895200-38904200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr19:38895200-38906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr19:38895200-38907800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:38895200-38908200	Weak transcription	Fetal Thymus	thymus
36	chr19:38895400-38897800	Strong transcription	Esophagus	oesophagus
37	chr19:38895400-38898000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:38895400-38898000	Strong transcription	Brain Hippocampus Middle	brain
39	chr19:38895400-38898000	Strong transcription	Colon Smooth Muscle	Colon
40	chr19:38895400-38898200	Strong transcription	Fetal Muscle Leg	muscle
41	chr19:38895400-38900000	Strong transcription	Fetal Intestine Small	intestine
42	chr19:38895400-38900000	Strong transcription	Fetal Stomach	stomach
43	chr19:38895400-38907800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr19:38895400-38908000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr19:38895600-38898000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:38895600-38898000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:38895600-38898000	Strong transcription	Adipose Nuclei	Adipose
48	chr19:38895600-38898000	Strong transcription	Brain Anterior Caudate	brain
49	chr19:38895600-38898000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr19:38895600-38898000	Strong transcription	Colonic Mucosa	Colon

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