Variant report

Variant	rs2965230
Chromosome Location	chr19:53751217-53751218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10401578	0.80[CHB][hapmap]
rs10404048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10413453	0.89[ASN][1000 genomes]
rs10417666	0.82[ASN][1000 genomes]
rs11084227	0.80[CHB][hapmap]
rs1129002	0.87[CHB][hapmap]
rs12981894	0.89[ASN][1000 genomes]
rs12984188	0.86[CHB][hapmap]
rs12984473	0.86[CHB][hapmap]
rs17272966	0.86[CHB][hapmap]
rs2865241	0.85[ASN][1000 genomes]
rs2914371	0.82[CHB][hapmap]
rs2914373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914376	0.86[CHB][hapmap]
rs2914378	0.86[CHB][hapmap]
rs2914379	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914382	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914383	0.80[CHB][hapmap]
rs2965221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965225	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965227	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965228	0.89[YRI][hapmap]
rs2965231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965235	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965241	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3097251	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111318	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3111320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4239497	0.89[ASN][1000 genomes]
rs4801972	0.98[ASN][1000 genomes]
rs4803068	0.89[ASN][1000 genomes]
rs4803070	0.83[ASN][1000 genomes]
rs4803073	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803075	0.82[EUR][1000 genomes]
rs4803076	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803077	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247982	1.00[CHB][hapmap]
rs7248781	0.96[ASN][1000 genomes]
rs7248812	0.96[ASN][1000 genomes]
rs7249931	0.97[ASN][1000 genomes]
rs7253646	0.98[ASN][1000 genomes]
rs7257238	0.91[ASN][1000 genomes]
rs8104393	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105607	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8109793	0.98[ASN][1000 genomes]
rs9788	1.00[CHB][hapmap];0.88[YRI][hapmap]

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:74 , 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	chr19:53743000-53756600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr19:53745200-53756600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:53747200-53752400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr19:53747400-53753600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:53747400-53754600	Weak transcription	HSMMtube	muscle
20	chr19:53747600-53753400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:53747600-53753400	Weak transcription	Pancreas	Pancrea
22	chr19:53747600-53753600	Weak transcription	Thymus	Thymus
23	chr19:53747600-53754400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:53747800-53753400	Weak transcription	Gastric	stomach
25	chr19:53747800-53753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:53747800-53753600	Weak transcription	Right Ventricle	heart
27	chr19:53747800-53755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:53747800-53757000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr19:53748400-53751600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:53748400-53757400	Weak transcription	Colonic Mucosa	Colon
31	chr19:53748800-53752200	Weak transcription	Osteobl	bone
32	chr19:53749400-53752400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:53749600-53751400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
34	chr19:53749600-53752800	ZNF genes & repeats	Brain Anterior Caudate	brain
35	chr19:53749600-53755800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
36	chr19:53749600-53756200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr19:53749800-53751600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
38	chr19:53749800-53752000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:53749800-53752600	Weak transcription	Fetal Stomach	stomach
40	chr19:53749800-53752800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
41	chr19:53749800-53756600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:53750000-53752400	Weak transcription	Dnd41	blood
43	chr19:53750000-53757200	Weak transcription	HUVEC	blood vessel
44	chr19:53750200-53751800	ZNF genes & repeats	Primary T cells from cord blood	blood
45	chr19:53750200-53752200	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr19:53750200-53756600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:53750400-53752200	Weak transcription	NHLF	lung
48	chr19:53750400-53754600	Weak transcription	Fetal Heart	heart
49	chr19:53750400-53755800	Strong transcription	HSMM	muscle
50	chr19:53750400-53759200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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