Variant report

Variant	rs60937535
Chromosome Location	chr19:52639323-52639324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52638083..52640348-chr19:52693399..52695139,2	MCF-7	breast:
2	chr19:52631135..52633164-chr19:52639000..52640822,2	K562	blood:
3	chr19:52633223..52639825-chr19:52641959..52644424,7	MCF-7	breast:
4	chr19:52598248..52599902-chr19:52638562..52641237,2	MCF-7	breast:
5	chr19:52636537..52639802-chr19:52640245..52644732,7	K562	blood:

Variant related genes	Relation type
ENSG00000204611	Chromatin interaction
ENSG00000197608	Chromatin interaction
ENSG00000256087	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12459201	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12459227	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59541557	0.94[EUR][1000 genomes]
rs60164622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61573127	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67170112	0.94[EUR][1000 genomes]
rs67602609	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67861844	0.94[EUR][1000 genomes]
rs8103346	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv3433050	chr19:52595705-52639973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52606800-52640200	ZNF genes & repeats	Liver	Liver
2	chr19:52609800-52640200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:52615200-52640200	ZNF genes & repeats	Fetal Brain Female	brain
4	chr19:52615600-52640200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:52616200-52640000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:52616200-52641200	ZNF genes & repeats	Dnd41	blood
7	chr19:52616200-52641400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:52616200-52641600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:52616400-52641400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:52617000-52640200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr19:52617200-52640200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:52617400-52641400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:52618000-52640200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:52624200-52640200	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr19:52626600-52640400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:52627200-52640200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:52628800-52639800	ZNF genes & repeats	Fetal Stomach	stomach
18	chr19:52628800-52641400	Weak transcription	Brain Substantia Nigra	brain
19	chr19:52629000-52641200	Weak transcription	Right Ventricle	heart
20	chr19:52629200-52640800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr19:52629400-52641200	Weak transcription	Colon Smooth Muscle	Colon
22	chr19:52629400-52641600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:52629600-52641800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:52629800-52641200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:52630600-52640200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:52630600-52640200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:52631000-52640800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:52631400-52641200	Weak transcription	K562	blood
29	chr19:52632000-52641200	Weak transcription	Brain Anterior Caudate	brain
30	chr19:52632200-52640200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr19:52632600-52640000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr19:52632800-52640200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
33	chr19:52633600-52641200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr19:52633600-52641600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:52633800-52641200	Weak transcription	Brain Angular Gyrus	brain
36	chr19:52633800-52641200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr19:52633800-52641200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:52633800-52641600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr19:52634000-52639400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:52634000-52640800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr19:52634000-52641000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:52634000-52641200	Weak transcription	Brain Hippocampus Middle	brain
43	chr19:52634000-52641200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr19:52634000-52641400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr19:52634000-52642000	Weak transcription	Small Intestine	intestine
46	chr19:52634200-52641200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr19:52634200-52641200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:52634200-52641200	Weak transcription	Aorta	Aorta
49	chr19:52634200-52641200	Weak transcription	Left Ventricle	heart
50	chr19:52634200-52641200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links