Variant report

Variant	rs10402799
Chromosome Location	chr19:19432905-19432906
allele	C/G
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19413906..19419021-chr19:19429875..19434162,7	K562	blood:
2	chr19:19431656..19433279-chr19:19456145..19458493,2	K562	blood:
3	chr19:19431090..19433292-chr19:19443001..19445440,2	MCF-7	breast:
4	chr19:19431266..19434636-chr19:19448982..19451713,3	MCF-7	breast:
5	chr19:19430154..19433018-chr19:19625258..19627975,2	K562	blood:
6	chr19:11848265..11850044-chr19:19430970..19433049,2	MCF-7	breast:
7	chr19:19431326..19434090-chr19:19651434..19653911,2	K562	blood:
8	chr19:19430396..19433402-chr19:19454872..19458235,4	MCF-7	breast:
9	chr19:19280644..19282541-chr19:19431552..19433735,2	MCF-7	breast:
10	chr19:19430075..19433378-chr19:19444857..19448772,4	K562	blood:
11	chr19:19312433..19314874-chr19:19432298..19433867,2	MCF-7	breast:
12	chr19:19304004..19306841-chr19:19429725..19433437,3	MCF-7	breast:
13	chr19:19430044..19433811-chr19:19447380..19449569,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105705	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000160161	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000258674	Chromatin interaction
ENSG00000184162	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000197933	Chromatin interaction
ENSG00000186010	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10408216	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10413309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10417312	0.89[AMR][1000 genomes]
rs10417715	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10422331	0.82[AFR][1000 genomes]
rs10422522	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10422620	0.82[AFR][1000 genomes]
rs10423747	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12327663	0.96[AFR][1000 genomes]
rs16996031	0.96[AFR][1000 genomes]
rs16996042	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2106699	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2315280	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28437425	0.92[AFR][1000 genomes]
rs28857503	0.92[AFR][1000 genomes]
rs55877107	0.85[AFR][1000 genomes]
rs56304704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56317107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60860168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7248765	1.00[AMR][1000 genomes]
rs7249940	1.00[AMR][1000 genomes]
rs73922864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8110508	0.90[AFR][1000 genomes];1.00[AMR][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	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19430400-19433200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19430400-19433200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:19430400-19433600	Active TSS	GM12878-XiMat	blood
4	chr19:19430600-19433200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:19430600-19433200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:19430800-19433200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:19431000-19433200	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr19:19431000-19433200	Active TSS	Fetal Brain Female	brain
9	chr19:19431000-19433200	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
10	chr19:19431600-19433000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr19:19432200-19433000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:19432200-19433000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr19:19432200-19433000	Flanking Active TSS	Brain Cingulate Gyrus	brain
14	chr19:19432200-19433000	Flanking Active TSS	Duodenum Mucosa	Duodenum
15	chr19:19432200-19433200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:19432200-19433400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:19432200-19433400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:19432200-19433400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:19432200-19433400	Flanking Active TSS	Dnd41	blood
20	chr19:19432400-19433000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:19432400-19433200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:19432400-19433200	Active TSS	HepG2	liver
23	chr19:19432400-19433400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr19:19432400-19433400	Enhancers	Spleen	Spleen
25	chr19:19432600-19433400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr19:19432600-19433400	Enhancers	Fetal Heart	heart
27	chr19:19432600-19433400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr19:19432600-19433800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:19432600-19445400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr19:19432800-19433000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:19432800-19433000	Enhancers	Primary T cells from cord blood	blood
32	chr19:19432800-19433000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:19432800-19433000	Enhancers	Brain Hippocampus Middle	brain
34	chr19:19432800-19433000	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr19:19432800-19433000	Enhancers	Stomach Mucosa	stomach
36	chr19:19432800-19433200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:19432800-19433200	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr19:19432800-19433200	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr19:19432800-19433200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr19:19432800-19433200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr19:19432800-19433200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:19432800-19433200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr19:19432800-19433200	Enhancers	Fetal Muscle Trunk	muscle
44	chr19:19432800-19433200	Weak transcription	Pancreas	Pancrea
45	chr19:19432800-19433200	Enhancers	Thymus	Thymus
46	chr19:19432800-19433400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:19432800-19433400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr19:19432800-19433400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:19432800-19433400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:19432800-19433400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links