Variant report

Variant	rs10404020
Chromosome Location	chr19:19096506-19096507
allele	C/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19049584..19053543-chr19:19093470..19096968,5	MCF-7	breast:
2	chr19:19042103..19043822-chr19:19095994..19097788,2	K562	blood:
3	chr19:19096426..19099301-chr19:19099737..19102756,3	MCF-7	breast:
4	chr19:19086874..19091371-chr19:19096444..19100736,4	K562	blood:
5	chr19:19096487..19099178-chr19:19102823..19104389,2	MCF-7	breast:
6	chr19:19031164..19034036-chr19:19094993..19099156,4	MCF-7	breast:
7	chr19:19039541..19041995-chr19:19096348..19099179,2	MCF-7	breast:
8	chr19:19028621..19032208-chr19:19096028..19099996,7	MCF-7	breast:
9	chr19:19094846..19096538-chr19:19098164..19100620,2	K562	blood:
10	chr19:19032960..19035455-chr19:19093521..19096915,3	MCF-7	breast:
11	chr19:19038588..19040520-chr19:19096486..19099319,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000064607	Chromatin interaction
ENSG00000105669	Chromatin interaction
ENSG00000051128	Chromatin interaction
ENSG00000269131	Chromatin interaction
ENSG00000269019	Chromatin interaction
ENSG00000105671	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10402411	0.80[AFR][1000 genomes]
rs10404879	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs10406282	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs10406341	0.83[AFR][1000 genomes]
rs10407260	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs10409265	0.92[YRI][hapmap];0.95[AFR][1000 genomes]
rs10409297	0.85[AFR][1000 genomes]
rs10409395	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs10412101	0.83[AFR][1000 genomes]
rs10413216	0.84[YRI][hapmap]
rs10414535	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs10414859	0.85[AFR][1000 genomes]
rs10415998	0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416041	0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs10416054	0.84[YRI][hapmap];0.83[AFR][1000 genomes]
rs10416240	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416250	0.83[AFR][1000 genomes]
rs10416730	0.83[AFR][1000 genomes]
rs10417310	0.83[AFR][1000 genomes]
rs10417682	0.83[AFR][1000 genomes]
rs10418688	0.83[AFR][1000 genomes]
rs10419114	0.83[AFR][1000 genomes]
rs10419307	0.83[AFR][1000 genomes]
rs10420479	0.84[YRI][hapmap]
rs10420559	0.84[YRI][hapmap]
rs10422238	0.81[AFR][1000 genomes]
rs10423129	0.83[AFR][1000 genomes]
rs10423504	0.82[AFR][1000 genomes]
rs10426131	0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs13344835	0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13345246	0.83[AFR][1000 genomes]
rs28416794	0.85[AFR][1000 genomes]
rs28421315	0.83[AFR][1000 genomes]
rs28445835	0.84[YRI][hapmap]
rs28475392	0.90[AFR][1000 genomes]
rs28477157	0.83[AFR][1000 genomes]
rs28477961	0.83[AFR][1000 genomes]
rs28507927	0.83[AFR][1000 genomes]
rs28530647	0.80[AFR][1000 genomes]
rs28533991	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28628081	0.83[AFR][1000 genomes]
rs28699197	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs28720008	0.83[AFR][1000 genomes]
rs35646935	0.83[AFR][1000 genomes]
rs6511012	0.84[YRI][hapmap]
rs7252172	0.82[AFR][1000 genomes]
rs8106189	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19084200-19107800	Weak transcription	Right Atrium	heart
2	chr19:19094200-19098000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr19:19094800-19097400	Weak transcription	Right Ventricle	heart
4	chr19:19094800-19097800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr19:19094800-19099200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:19095200-19096800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:19095200-19097600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr19:19095400-19097600	Enhancers	HUVEC	blood vessel
9	chr19:19095400-19098000	Enhancers	Adipose Nuclei	Adipose
10	chr19:19095600-19096800	Enhancers	Primary hematopoietic stem cells	blood
11	chr19:19095600-19097800	Enhancers	Fetal Brain Male	brain
12	chr19:19095600-19097800	Bivalent Enhancer	Fetal Stomach	stomach
13	chr19:19095600-19098000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr19:19095600-19098000	Enhancers	Fetal Muscle Leg	muscle
15	chr19:19095800-19096800	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr19:19095800-19097400	Weak transcription	Lung	lung
17	chr19:19095800-19098000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr19:19095800-19098000	Enhancers	Brain Substantia Nigra	brain
19	chr19:19096000-19096800	Enhancers	Fetal Lung	lung
20	chr19:19096000-19097600	Enhancers	Spleen	Spleen
21	chr19:19096000-19098000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:19096000-19098000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:19096200-19096600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
24	chr19:19096200-19096600	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr19:19096200-19096600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr19:19096200-19096600	Bivalent Enhancer	Fetal Thymus	thymus
27	chr19:19096200-19101600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr19:19096200-19104000	Weak transcription	Primary B cells from cord blood	blood
29	chr19:19096400-19096600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:19096400-19096600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr19:19096400-19097400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr19:19096400-19097400	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr19:19096400-19097600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:19096400-19097600	Enhancers	Brain Germinal Matrix	brain
35	chr19:19096400-19098000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:19096400-19098000	Enhancers	Brain Angular Gyrus	brain
37	chr19:19096400-19098000	Enhancers	Brain Anterior Caudate	brain
38	chr19:19096400-19098000	Enhancers	Brain Hippocampus Middle	brain
39	chr19:19096400-19100800	Weak transcription	Fetal Brain Female	brain
40	chr19:19096400-19101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:19096400-19102200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr19:19096400-19103400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:19096400-19103600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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