Variant report

Variant	rs2571164
Chromosome Location	chr19:44949987-44949988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44943302..44945039-chr19:44949039..44951597,2	MCF-7	breast:
2	chr19:44945678..44948451-chr19:44948958..44951509,3	MCF-7	breast:
3	chr19:44942698..44944302-chr19:44948026..44950274,2	MCF-7	breast:
4	chr19:44948832..44950622-chr19:44950941..44952860,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167383	Chromatin interaction
ENSG00000267188	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2466416	0.88[ASN][1000 genomes]
rs2571158	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2571159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571162	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571163	1.00[ASN][1000 genomes]
rs2571166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571169	1.00[ASN][1000 genomes]
rs2571170	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2571174	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722693	0.97[ASN][1000 genomes]
rs2722697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722699	1.00[ASN][1000 genomes]
rs2722700	1.00[ASN][1000 genomes]
rs2722701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2722702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2734453	0.97[ASN][1000 genomes]
rs2734457	0.97[ASN][1000 genomes]
rs4802224	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912112	chr19:44853707-45011727	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv912114	chr19:44858776-45002563	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1061350	chr19:44869075-45035469	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44928400-44951800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:44932000-44953200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr19:44934600-44950800	Weak transcription	Hela-S3	cervix
4	chr19:44936000-44951400	Weak transcription	Fetal Heart	heart
5	chr19:44936400-44952000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:44937400-44951800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr19:44938400-44951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:44938800-44951600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:44940000-44950600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:44940200-44951200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr19:44940600-44951800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:44940600-44951800	Weak transcription	Fetal Thymus	thymus
13	chr19:44941600-44950400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:44942000-44950200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:44942000-44950400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:44942000-44950800	ZNF genes & repeats	Fetal Brain Female	brain
17	chr19:44942200-44951800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr19:44942400-44950400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
19	chr19:44942400-44951400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:44942600-44952000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:44944200-44950400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:44944400-44952200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
23	chr19:44944600-44952200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr19:44945000-44951200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
25	chr19:44945200-44951200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:44945400-44950600	Strong transcription	HMEC	breast
27	chr19:44945400-44951200	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr19:44945600-44951800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:44945800-44950400	ZNF genes & repeats	Adipose Nuclei	Adipose
30	chr19:44945800-44951000	Strong transcription	NHLF	lung
31	chr19:44946000-44950600	ZNF genes & repeats	Ovary	ovary
32	chr19:44946200-44951800	Weak transcription	HUVEC	blood vessel
33	chr19:44946400-44950400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:44946400-44950400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
35	chr19:44946400-44950400	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr19:44946400-44950400	ZNF genes & repeats	Fetal Stomach	stomach
37	chr19:44946400-44950400	ZNF genes & repeats	Left Ventricle	heart
38	chr19:44946400-44951400	ZNF genes & repeats	Brain Germinal Matrix	brain
39	chr19:44946400-44953000	ZNF genes & repeats	Aorta	Aorta
40	chr19:44946600-44950200	ZNF genes & repeats	Lung	lung
41	chr19:44947000-44950200	Weak transcription	Fetal Kidney	kidney
42	chr19:44947000-44950400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:44947000-44951800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr19:44947400-44951200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:44947400-44951400	Weak transcription	Right Ventricle	heart
46	chr19:44947400-44951400	Weak transcription	NHDF-Ad	bronchial
47	chr19:44947600-44950000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr19:44947800-44951800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:44948200-44950400	ZNF genes & repeats	Pancreas	Pancrea
50	chr19:44948200-44950400	ZNF genes & repeats	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links