Variant report

Variant	rs59498150
Chromosome Location	chr19:21237325-21237326
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:41381927..41383535-chr19:21236269..21237789,2	MCF-7	breast:
2	chr17:41381905..41383742-chr19:21236269..21237789,3	K562	blood:

Variant related genes	Relation type
ENSG00000236383	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10401988	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10402207	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10406243	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10406276	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10406390	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407928	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10411360	0.83[AMR][1000 genomes]
rs10413561	0.83[AMR][1000 genomes]
rs10424613	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425562	0.83[AMR][1000 genomes]
rs10425664	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11880964	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13345905	0.83[AMR][1000 genomes]
rs28394595	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28500793	0.83[AMR][1000 genomes]
rs28635135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28858186	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35569945	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7247708	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7248199	0.88[AFR][1000 genomes]
rs7250059	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73531822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73537721	0.83[AMR][1000 genomes]
rs9941493	0.88[AFR][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	nsv1062776	chr19:20818886-21273361	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv932110	chr19:20818886-21278952	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	esv2763043	chr19:20818886-21290543	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv817536	chr19:21041855-21348237	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	esv1850387	chr19:21109758-21294264	Active TSS ZNF genes & repeats Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv911411	chr19:21184533-21263518	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv578949	chr19:21190572-21244049	ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv960811	chr19:21200306-21371757	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
10	esv3399352	chr19:21232738-21423323	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
11	esv1805898	chr19:21233245-21256249	Strong transcription ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
12	nsv911412	chr19:21233388-21297358	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21204400-21264800	Weak transcription	Right Ventricle	heart
2	chr19:21204600-21239800	Weak transcription	Colon Smooth Muscle	Colon
3	chr19:21206200-21241600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:21207200-21239400	Weak transcription	Hela-S3	cervix
5	chr19:21212000-21241400	Weak transcription	Fetal Heart	heart
6	chr19:21221400-21242000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:21222400-21242200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr19:21223000-21244200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:21227400-21241400	ZNF genes & repeats	GM12878-XiMat	blood
10	chr19:21227800-21247200	Weak transcription	HepG2	liver
11	chr19:21230600-21248400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:21230800-21238600	Weak transcription	NHLF	lung
13	chr19:21230800-21240400	Weak transcription	HSMMtube	muscle
14	chr19:21230800-21243000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:21231000-21238200	Weak transcription	Stomach Mucosa	stomach
16	chr19:21231000-21239000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:21231600-21239400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
18	chr19:21231600-21241000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:21231600-21241600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
20	chr19:21231800-21238600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:21231800-21244600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:21232200-21237400	ZNF genes & repeats	Primary B cells from cord blood	blood
23	chr19:21232200-21238200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:21232200-21241000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
25	chr19:21232200-21241000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
26	chr19:21232200-21241200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
27	chr19:21232200-21242200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr19:21232200-21242400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr19:21232200-21243600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:21232600-21238000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr19:21232600-21238400	Weak transcription	Gastric	stomach
32	chr19:21232800-21241000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:21233800-21238200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:21233800-21238800	Weak transcription	Fetal Brain Male	brain
35	chr19:21234200-21237800	ZNF genes & repeats	Adipose Nuclei	Adipose
36	chr19:21234200-21242400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:21234600-21241400	ZNF genes & repeats	Primary T cells from cord blood	blood
38	chr19:21234800-21238400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:21235000-21237400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
40	chr19:21235000-21241200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
41	chr19:21235200-21238400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:21235200-21239600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:21235200-21239800	ZNF genes & repeats	Dnd41	blood
44	chr19:21235200-21240200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:21235200-21242000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:21235200-21242600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr19:21235400-21237400	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr19:21235400-21238400	Strong transcription	HSMM	muscle
49	chr19:21235400-21240000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:21235400-21241000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links