Variant report

Variant	rs73934439
Chromosome Location	chr19:52873568-52873569
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52771473..52773658-chr19:52872286..52874915,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs56370398	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7252317	0.81[AMR][1000 genomes]
rs7254826	0.90[AMR][1000 genomes]
rs7256723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7256752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7256760	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7260092	0.90[AMR][1000 genomes]
rs73934440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8109180	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52865200-52875400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:52866600-52875400	ZNF genes & repeats	Liver	Liver
3	chr19:52871200-52876400	Weak transcription	Dnd41	blood
4	chr19:52872400-52873600	Active TSS	Monocytes-CD14+_RO01746	blood
5	chr19:52872400-52874000	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr19:52872600-52873800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:52872600-52873800	Active TSS	Fetal Brain Female	brain
8	chr19:52872600-52873800	Active TSS	Right Ventricle	heart
9	chr19:52872600-52874000	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr19:52872600-52874000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:52872600-52874000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:52872600-52874000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:52872600-52874000	Active TSS	Duodenum Mucosa	Duodenum
14	chr19:52872600-52874000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr19:52872600-52874000	Active TSS	Fetal Intestine Small	intestine
16	chr19:52872600-52874000	Active TSS	Fetal Muscle Trunk	muscle
17	chr19:52872600-52874000	Active TSS	Fetal Muscle Leg	muscle
18	chr19:52872600-52874000	Active TSS	Fetal Stomach	stomach
19	chr19:52872600-52874000	Active TSS	Right Atrium	heart
20	chr19:52872600-52874000	Active TSS	Thymus	Thymus
21	chr19:52872600-52874200	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr19:52872600-52874400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:52872600-52874400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr19:52872600-52874400	Active TSS	Fetal Kidney	kidney
25	chr19:52872600-52874800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:52872800-52873600	Active TSS	Primary B cells from cord blood	blood
27	chr19:52872800-52873600	Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr19:52872800-52873600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr19:52872800-52873600	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr19:52872800-52873600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr19:52872800-52873600	Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr19:52872800-52873600	Active TSS	Colonic Mucosa	Colon
33	chr19:52872800-52873600	Active TSS	Fetal Brain Male	brain
34	chr19:52872800-52873800	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:52872800-52873800	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr19:52872800-52873800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
37	chr19:52872800-52873800	Active TSS	Aorta	Aorta
38	chr19:52872800-52873800	Active TSS	Brain Angular Gyrus	brain
39	chr19:52872800-52873800	Active TSS	Brain Substantia Nigra	brain
40	chr19:52872800-52873800	Active TSS	Colon Smooth Muscle	Colon
41	chr19:52872800-52873800	Active TSS	Gastric	stomach
42	chr19:52872800-52873800	ZNF genes & repeats	Lung	lung
43	chr19:52872800-52873800	Active TSS	Stomach Mucosa	stomach
44	chr19:52872800-52874000	Active TSS	H1 Cell Line	embryonic stem cell
45	chr19:52872800-52874000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr19:52872800-52874000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:52872800-52874000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:52872800-52874000	Active TSS	H9 Cell Line	embryonic stem cell
49	chr19:52872800-52874000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:52872800-52874000	Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links