Variant report

Variant	rs56971820
Chromosome Location	chr19:18215917-18215918
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18215138..18216766-chr19:18223836..18225347,2	MCF-7	breast:
2	chr19:18207064..18208834-chr19:18213992..18216646,2	MCF-7	breast:
3	chr19:18214257..18217360-chr19:18228399..18230348,3	MCF-7	breast:
4	chr19:18185895..18188337-chr19:18214059..18216560,2	K562	blood:
5	chr19:18208517..18210174-chr19:18213137..18216099,2	K562	blood:

Variant related genes	Relation type
ENSG00000099308	Chromatin interaction
ENSG00000096996	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11086089	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11665905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667112	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11667917	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11670228	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11672366	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11673702	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs273496	0.84[EUR][1000 genomes]
rs273503	0.90[EUR][1000 genomes]
rs273504	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs273505	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs273506	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs273508	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs273512	0.83[EUR][1000 genomes]
rs4808746	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58049250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121155	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121158	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62123561	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7249862	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	nsv470130	chr19:18047283-18234587	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
6	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv911241	chr19:18193191-18304700	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv911242	chr19:18201757-18304700	Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv911243	chr19:18206681-18283501	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv911244	chr19:18206681-18304700	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv911245	chr19:18206681-18338101	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv833774	chr19:18213761-18295329	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv833775	chr19:18213761-18390074	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18213600-18216000	Enhancers	Fetal Brain Male	brain
2	chr19:18214200-18216000	Enhancers	Fetal Stomach	stomach
3	chr19:18214400-18216000	Enhancers	Spleen	Spleen
4	chr19:18215000-18216000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:18215000-18216000	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr19:18215000-18216000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr19:18215600-18216000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr19:18215600-18216000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
9	chr19:18215600-18216000	Enhancers	Fetal Thymus	thymus
10	chr19:18215600-18216600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:18215600-18219600	Weak transcription	Gastric	stomach
12	chr19:18215600-18220400	Weak transcription	Esophagus	oesophagus
13	chr19:18215600-18220400	Weak transcription	Lung	lung
14	chr19:18215800-18216000	Enhancers	H1 Cell Line	embryonic stem cell
15	chr19:18215800-18216000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:18215800-18216000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:18215800-18216000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr19:18215800-18216000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr19:18215800-18216000	Enhancers	Primary hematopoietic stem cells	blood
20	chr19:18215800-18216000	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr19:18215800-18216000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:18215800-18216000	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr19:18215800-18216000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr19:18215800-18216000	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr19:18215800-18216000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr19:18215800-18216000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr19:18215800-18216000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:18215800-18216000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr19:18215800-18216000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr19:18215800-18216000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:18215800-18216000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:18215800-18216000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:18215800-18216000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr19:18215800-18216000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:18215800-18216000	Enhancers	Aorta	Aorta
36	chr19:18215800-18216000	Enhancers	Liver	Liver
37	chr19:18215800-18216000	Active TSS	Brain Cingulate Gyrus	brain
38	chr19:18215800-18216000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:18215800-18216000	Enhancers	Duodenum Mucosa	Duodenum
40	chr19:18215800-18216000	Enhancers	Fetal Intestine Large	intestine
41	chr19:18215800-18216000	Enhancers	Fetal Intestine Small	intestine
42	chr19:18215800-18216000	Enhancers	Placenta	Placenta
43	chr19:18215800-18216000	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr19:18215800-18216000	Enhancers	Right Ventricle	heart
45	chr19:18215800-18216000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
46	chr19:18215800-18216000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
47	chr19:18215800-18216000	Enhancers	GM12878-XiMat	blood
48	chr19:18215800-18216000	Enhancers	HepG2	liver
49	chr19:18215800-18216000	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr19:18215800-18216200	Enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links