Variant report

Variant	rs2965229
Chromosome Location	chr19:53750613-53750614
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10404048	0.80[EUR][1000 genomes]
rs2965226	0.87[AFR][1000 genomes]
rs2965227	0.87[AFR][1000 genomes]
rs2965228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111320	0.86[AFR][1000 genomes]
rs4801972	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8109793	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1064604	chr19:53730688-53751243	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv580079	chr19:53732590-53756120	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1055236	chr19:53739483-53778339	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1059899	chr19:53744560-53768337	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1064070	chr19:53744560-53769702	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53733600-53755200	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:53733600-53755800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:53735800-53756200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:53737400-53757600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:53738800-53756600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
6	chr19:53739400-53755200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:53739600-53756200	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:53740000-53756400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr19:53740000-53756600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
10	chr19:53740000-53756800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:53740200-53752600	ZNF genes & repeats	Brain Hippocampus Middle	brain
12	chr19:53740200-53756800	ZNF genes & repeats	Fetal Lung	lung
13	chr19:53740200-53757600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:53740400-53756800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr19:53743000-53750800	ZNF genes & repeats	Fetal Intestine Large	intestine
16	chr19:53743000-53756600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr19:53745200-53756600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:53747200-53752400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr19:53747400-53753600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:53747400-53754600	Weak transcription	HSMMtube	muscle
21	chr19:53747600-53753400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr19:53747600-53753400	Weak transcription	Pancreas	Pancrea
23	chr19:53747600-53753600	Weak transcription	Thymus	Thymus
24	chr19:53747600-53754400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr19:53747800-53753400	Weak transcription	Gastric	stomach
26	chr19:53747800-53753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:53747800-53753600	Weak transcription	Right Ventricle	heart
28	chr19:53747800-53755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:53747800-53757000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr19:53748400-53751600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:53748400-53757400	Weak transcription	Colonic Mucosa	Colon
32	chr19:53748800-53750800	Strong transcription	Left Ventricle	heart
33	chr19:53748800-53752200	Weak transcription	Osteobl	bone
34	chr19:53749400-53752400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:53749600-53751400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
36	chr19:53749600-53752800	ZNF genes & repeats	Brain Anterior Caudate	brain
37	chr19:53749600-53755800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr19:53749600-53756200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
39	chr19:53749800-53750800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr19:53749800-53751000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr19:53749800-53751000	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr19:53749800-53751600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
43	chr19:53749800-53752000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:53749800-53752600	Weak transcription	Fetal Stomach	stomach
45	chr19:53749800-53752800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
46	chr19:53749800-53756600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:53750000-53750800	ZNF genes & repeats	Placenta	Placenta
48	chr19:53750000-53752400	Weak transcription	Dnd41	blood
49	chr19:53750000-53757200	Weak transcription	HUVEC	blood vessel
50	chr19:53750200-53750800	ZNF genes & repeats	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links