Variant report

Variant	rs10412805
Chromosome Location	chr19:53577214-53577215
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53576657..53578759-chr19:53604780..53606841,2	MCF-7	breast:
2	chr19:53571470..53573279-chr19:53575256..53577909,2	K562	blood:

Variant related genes	Relation type
ENSG00000170949	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10406237	1.00[ASN][1000 genomes]
rs10409615	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410030	1.00[ASN][1000 genomes]
rs10418505	1.00[ASN][1000 genomes]
rs16984438	1.00[ASN][1000 genomes]
rs16984443	1.00[ASN][1000 genomes]
rs16984486	1.00[ASN][1000 genomes]
rs28368410	1.00[ASN][1000 genomes]
rs28528321	1.00[ASN][1000 genomes]
rs28661145	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28662846	1.00[ASN][1000 genomes]
rs28691095	1.00[ASN][1000 genomes]
rs28701520	1.00[ASN][1000 genomes]
rs28726276	1.00[ASN][1000 genomes]
rs58143828	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509725	1.00[ASN][1000 genomes]
rs7247568	1.00[ASN][1000 genomes]
rs7253566	1.00[ASN][1000 genomes]
rs73935216	1.00[ASN][1000 genomes]
rs73935236	1.00[ASN][1000 genomes]
rs8099848	1.00[ASN][1000 genomes]
rs8100134	1.00[ASN][1000 genomes]
rs8102799	1.00[ASN][1000 genomes]
rs8113824	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
4	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv963073	chr19:53576593-53580049	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53564600-53586800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
2	chr19:53564800-53586600	ZNF genes & repeats	Liver	Liver
3	chr19:53566200-53577400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:53568000-53580600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
5	chr19:53568000-53586400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:53568200-53580600	ZNF genes & repeats	Lung	lung
7	chr19:53568400-53577800	ZNF genes & repeats	Fetal Intestine Large	intestine
8	chr19:53568400-53580600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:53568400-53588600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:53569000-53579200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr19:53569400-53578600	Strong transcription	Placenta Amnion	Placenta Amnion
12	chr19:53569600-53579400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:53570000-53582000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:53570200-53579200	ZNF genes & repeats	Ovary	ovary
15	chr19:53570200-53580600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
16	chr19:53570200-53580800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
17	chr19:53570200-53587400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:53570400-53578400	ZNF genes & repeats	Primary B cells from cord blood	blood
19	chr19:53570400-53578400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:53570400-53578800	ZNF genes & repeats	Thymus	Thymus
21	chr19:53570400-53580400	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:53570600-53589600	ZNF genes & repeats	GM12878-XiMat	blood
23	chr19:53571000-53579200	ZNF genes & repeats	Aorta	Aorta
24	chr19:53571000-53580600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
25	chr19:53571000-53587200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr19:53571400-53577600	ZNF genes & repeats	Spleen	Spleen
27	chr19:53571400-53580600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
28	chr19:53571800-53577600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
29	chr19:53571800-53579200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:53571800-53581200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
31	chr19:53571800-53583400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:53571800-53586000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
33	chr19:53571800-53586600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
34	chr19:53572000-53579200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:53572200-53580400	ZNF genes & repeats	Esophagus	oesophagus
36	chr19:53572600-53579400	Strong transcription	Brain Cingulate Gyrus	brain
37	chr19:53573200-53578600	Strong transcription	Brain Hippocampus Middle	brain
38	chr19:53573400-53578200	Strong transcription	Fetal Kidney	kidney
39	chr19:53573400-53578400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr19:53573400-53578400	Strong transcription	Brain Germinal Matrix	brain
41	chr19:53573400-53579200	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr19:53573400-53579600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr19:53573400-53579800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr19:53573400-53580000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr19:53573400-53580400	Strong transcription	Left Ventricle	heart
46	chr19:53573400-53580400	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr19:53573400-53580800	Strong transcription	Dnd41	blood
48	chr19:53573600-53578200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
49	chr19:53573600-53578600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:53573600-53579400	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links