Variant report

Variant	rs59000923
Chromosome Location	chr19:44007786-44007787
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:43997566..43999974-chr19:44006795..44009700,2	K562	blood:
2	chr19:43977180..43982299-chr19:44003653..44008245,6	K562	blood:
3	chr19:43997566..43999110-chr19:44006795..44008578,2	K562	blood:
4	chr19:43967204..43969877-chr19:44006593..44010322,9	MCF-7	breast:
5	chr19:44006496..44008143-chr19:44098024..44100658,2	MCF-7	breast:
6	chr19:43966113..43971089-chr19:44005040..44010546,6	K562	blood:
7	chr19:44007568..44009583-chr19:44036201..44039639,3	MCF-7	breast:
8	chr19:44005750..44008125-chr19:44129589..44132282,2	K562	blood:
9	chr19:43965066..43971111-chr19:44006791..44009897,14	MCF-7	breast:
10	chr19:44006689..44009864-chr19:44027261..44031051,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105767	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000124466	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000176472	Chromatin interaction
ENSG00000176531	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12460021	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12979907	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12980646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12981023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102954	0.87[EUR][1000 genomes]
rs34352751	0.80[EUR][1000 genomes]
rs34977009	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35016410	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35485252	0.87[EUR][1000 genomes]
rs36034157	0.81[EUR][1000 genomes]
rs36075334	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3810381	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4507015	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4544340	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4802183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802185	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59827264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61607741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509094	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71362654	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7248927	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7252962	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7253177	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8100211	0.87[EUR][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	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer 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	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	esv2762041	chr19:43986023-44014457	Strong transcription Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59000923	LOC653583///PHLDB3	Cis_1M	lymphoblastoid	RTeQTL
rs59000923	ETHE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44000000-44008000	Weak transcription	Small Intestine	intestine
2	chr19:44002000-44007800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr19:44005800-44007800	Enhancers	Spleen	Spleen
4	chr19:44006000-44008200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:44006200-44008600	Active TSS	Colonic Mucosa	Colon
6	chr19:44006400-44007800	Enhancers	Fetal Heart	heart
7	chr19:44006400-44007800	Weak transcription	Gastric	stomach
8	chr19:44006600-44007800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:44006600-44007800	Weak transcription	Lung	lung
10	chr19:44006600-44008800	Active TSS	Fetal Brain Female	brain
11	chr19:44006800-44007800	Flanking Active TSS	Liver	Liver
12	chr19:44007000-44007800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr19:44007000-44007800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr19:44007000-44007800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr19:44007000-44007800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:44007000-44007800	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr19:44007000-44007800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr19:44007000-44008000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:44007000-44008000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:44007000-44008000	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr19:44007000-44008000	Flanking Active TSS	HMEC	breast
22	chr19:44007000-44009000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr19:44007000-44009200	Active TSS	Esophagus	oesophagus
24	chr19:44007000-44009200	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr19:44007200-44007800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:44007200-44007800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr19:44007200-44007800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:44007200-44007800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:44007200-44007800	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr19:44007200-44007800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
31	chr19:44007200-44007800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:44007200-44007800	Flanking Active TSS	Stomach Smooth Muscle	stomach
33	chr19:44007200-44008000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr19:44007200-44008200	Flanking Active TSS	Dnd41	blood
35	chr19:44007200-44009000	Active TSS	Brain Anterior Caudate	brain
36	chr19:44007200-44009200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:44007200-44009200	Active TSS	Rectal Smooth Muscle	rectum
38	chr19:44007200-44009400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr19:44007400-44007800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:44007400-44007800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:44007400-44007800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
42	chr19:44007400-44007800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr19:44007400-44007800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:44007400-44007800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:44007400-44007800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr19:44007400-44007800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr19:44007400-44007800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr19:44007400-44007800	Flanking Active TSS	Thymus	Thymus
49	chr19:44007400-44007800	Flanking Active TSS	Hela-S3	cervix
50	chr19:44007400-44007800	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links