Variant report

Variant	rs10401969
Chromosome Location	chr19:19407718-19407719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19406549..19409786-chr19:19410836..19415157,5	K562	blood:
2	chr19:19406475..19408221-chr19:19410645..19412336,2	K562	blood:

Variant related genes	Relation type
ENSG00000105705	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11085259	0.84[YRI][hapmap]
rs11668104	0.93[AFR][1000 genomes]
rs12459676	0.83[AFR][1000 genomes]
rs12979148	0.91[AFR][1000 genomes]
rs2023883	0.89[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2074301	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs2228603	0.89[CEU][hapmap]
rs2240117	0.96[AFR][1000 genomes]
rs2301668	0.84[YRI][hapmap]
rs4808194	0.82[AFR][1000 genomes]
rs58542926	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72999033	0.90[EUR][1000 genomes]
rs73001065	0.83[EUR][1000 genomes]
rs739846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8105094	0.83[LWK][hapmap];0.84[YRI][hapmap]
rs8105984	0.86[LWK][hapmap];0.89[YRI][hapmap]
rs8107974	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8108647	0.84[YRI][hapmap]

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	nsv911304	chr19:19303802-19408164	Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	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

Variant related diseases (count:9)

Disease	PMID	Source
Cholesterol, total	24097068	GWAS catalog
Cholesterol, total	20686565	GWAS catalog
LDL cholesterol	20864672	GWAS catalog
Triglycerides	20686565	GWAS catalog
LDL cholesterol	24097068	GWAS catalog
Hepatic lipid content in extreme obesity	25246029	GWAS catalog
LDL cholesterol	19060906	GWAS catalog
LDL cholesterol	20686565	GWAS catalog
Triglycerides	24097068	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10401969	ATP13A1	cis	multi-tissue	Pritchard
rs10401969	KIAA0892	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19384400-19430600	Weak transcription	Right Atrium	heart
2	chr19:19385400-19409800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr19:19385400-19428400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:19385600-19410000	Strong transcription	Stomach Smooth Muscle	stomach
5	chr19:19385800-19409600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:19385800-19410000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr19:19386000-19415200	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr19:19386200-19408200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:19386200-19421000	Weak transcription	Stomach Mucosa	stomach
10	chr19:19386800-19428400	Strong transcription	Fetal Intestine Small	intestine
11	chr19:19387000-19408600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:19387200-19408400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:19388000-19429000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:19389200-19412800	Weak transcription	HMEC	breast
15	chr19:19389600-19419000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:19390400-19411800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr19:19390400-19412200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr19:19390800-19430000	Weak transcription	Psoas Muscle	Psoas
19	chr19:19392400-19415000	Weak transcription	Fetal Heart	heart
20	chr19:19392600-19412600	Weak transcription	Fetal Brain Male	brain
21	chr19:19393800-19418600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr19:19394400-19408600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:19394600-19409800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr19:19395600-19412800	Weak transcription	NHEK	skin
25	chr19:19397200-19420800	Weak transcription	NHDF-Ad	bronchial
26	chr19:19397400-19418600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr19:19397600-19416400	Weak transcription	Small Intestine	intestine
28	chr19:19398000-19426800	Weak transcription	K562	blood
29	chr19:19398200-19411200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:19398400-19412000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:19400400-19408600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr19:19401200-19411200	Weak transcription	Colonic Mucosa	Colon
33	chr19:19401200-19412200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:19401200-19412200	Weak transcription	Brain Angular Gyrus	brain
35	chr19:19401400-19413400	Weak transcription	HepG2	liver
36	chr19:19402400-19427600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:19402400-19427800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr19:19402600-19427400	Strong transcription	Lung	lung
39	chr19:19402800-19409400	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:19402800-19410200	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr19:19402800-19427600	Strong transcription	Fetal Intestine Large	intestine
42	chr19:19402800-19428600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:19403000-19408200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr19:19403000-19409600	Strong transcription	Primary T cells from cord blood	blood
45	chr19:19403000-19427800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:19403200-19408000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:19403200-19409000	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr19:19403200-19409600	Strong transcription	Brain Anterior Caudate	brain
49	chr19:19403200-19413800	Strong transcription	Fetal Brain Female	brain
50	chr19:19403200-19421600	Strong transcription	Brain Germinal Matrix	brain

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