Variant report

Variant	rs2965244
Chromosome Location	chr19:53756871-53756872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53756061..53758221-chr19:53835400..53837964,2	K562	blood:

Variant related genes	Relation type
ENSG00000213799	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11084228	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1129002	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11666631	0.82[ASN][1000 genomes]
rs12982260	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12984188	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12984473	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17272966	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28411117	0.88[ASN][1000 genomes]
rs2865241	0.83[ASN][1000 genomes]
rs2914371	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914372	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2914376	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2914377	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2914378	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2914383	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2914384	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2965222	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2965236	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2965237	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2965238	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2965240	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2965242	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2965243	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3097248	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3111319	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803071	0.87[ASN][1000 genomes]
rs4803080	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55779655	0.87[ASN][1000 genomes]
rs62117791	0.86[ASN][1000 genomes]
rs8113436	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
11	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
12	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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53737400-53757600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:53740200-53757600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:53747800-53757000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:53748400-53757400	Weak transcription	Colonic Mucosa	Colon
5	chr19:53750000-53757200	Weak transcription	HUVEC	blood vessel
6	chr19:53750400-53759200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:53750600-53757600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:53751200-53757400	ZNF genes & repeats	Primary B cells from cord blood	blood
9	chr19:53752000-53757000	ZNF genes & repeats	Fetal Intestine Large	intestine
10	chr19:53752000-53757200	Weak transcription	NH-A	brain
11	chr19:53752400-53759400	ZNF genes & repeats	Liver	Liver
12	chr19:53752600-53757400	Weak transcription	Stomach Mucosa	stomach
13	chr19:53753600-53757400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
14	chr19:53753600-53759000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
15	chr19:53753800-53757600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:53754000-53757400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr19:53754000-53757600	Weak transcription	Esophagus	oesophagus
18	chr19:53754600-53757600	Weak transcription	Gastric	stomach
19	chr19:53754800-53757400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr19:53755000-53757200	Weak transcription	Fetal Brain Male	brain
21	chr19:53755000-53757400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:53755200-53757400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:53755400-53757200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr19:53755400-53757200	Weak transcription	NHEK	skin
25	chr19:53755400-53757200	Weak transcription	NHLF	lung
26	chr19:53755400-53757400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr19:53755400-53757600	Weak transcription	Pancreas	Pancrea
28	chr19:53755600-53757200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr19:53755600-53757200	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:53755600-53757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:53755800-53757000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:53755800-53757000	Weak transcription	Fetal Kidney	kidney
33	chr19:53755800-53757200	Weak transcription	Colon Smooth Muscle	Colon
34	chr19:53755800-53757400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:53755800-53757400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr19:53755800-53757400	Weak transcription	HSMM	muscle
37	chr19:53755800-53757600	Weak transcription	Lung	lung
38	chr19:53756000-53757000	Weak transcription	Brain Anterior Caudate	brain
39	chr19:53756000-53757000	Weak transcription	NHDF-Ad	bronchial
40	chr19:53756000-53757200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr19:53756000-53757200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:53756000-53757200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:53756000-53757200	Weak transcription	Adipose Nuclei	Adipose
44	chr19:53756000-53757200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:53756000-53757200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr19:53756000-53757200	Weak transcription	Right Ventricle	heart
47	chr19:53756000-53757200	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:53756000-53757200	Weak transcription	Thymus	Thymus
49	chr19:53756000-53757400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:53756000-53757400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links