Variant report

Variant	rs10405475
Chromosome Location	chr19:19587985-19587986
allele	G/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: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	chr19:19492400..19494555-chr19:19586147..19589015,3	MCF-7	breast:
2	chr19:19587218..19589971-chr19:19595669..19597695,2	K562	blood:
3	chr19:19587338..19590282-chr19:19595416..19599165,3	MCF-7	breast:
4	chr19:19571238..19573571-chr19:19586807..19589450,2	MCF-7	breast:
5	chr19:19487227..19491094-chr19:19586686..19591214,5	MCF-7	breast:
6	chr19:19584315..19588308-chr19:19588802..19591974,4	K562	blood:
7	chr19:19495565..19498891-chr19:19586187..19588694,3	MCF-7	breast:
8	chr19:19561186..19563740-chr19:19587907..19590423,2	K562	blood:
9	chr19:19520080..19522054-chr19:19587916..19589786,2	K562	blood:
10	chr19:19585281..19589285-chr19:19590381..19594944,7	K562	blood:
11	chr19:19579004..19580878-chr19:19585404..19588085,2	MCF-7	breast:
12	chr19:19586797..19588345-chr19:19599482..19602199,2	K562	blood:
13	chr19:19519872..19522275-chr19:19586096..19589416,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000167491	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10401822	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403737	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10412351	1.00[AFR][1000 genomes]
rs10413582	1.00[AMR][1000 genomes]
rs10416335	0.92[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10417715	0.92[YRI][hapmap]
rs10421166	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423535	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10425164	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425574	1.00[AMR][1000 genomes]
rs13344439	0.89[AMR][1000 genomes]
rs16996031	0.84[YRI][hapmap]
rs16996042	0.92[YRI][hapmap]
rs16996102	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55927831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59344441	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60455087	0.89[AMR][1000 genomes]
rs73922887	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922890	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922896	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9304961	0.89[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19577800-19598000	Weak transcription	Ovary	ovary
2	chr19:19579200-19598000	Weak transcription	Small Intestine	intestine
3	chr19:19579400-19599400	Weak transcription	Brain Angular Gyrus	brain
4	chr19:19579800-19591000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:19579800-19593400	Weak transcription	Fetal Kidney	kidney
6	chr19:19579800-19595600	Weak transcription	Osteobl	bone
7	chr19:19579800-19595800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:19579800-19595800	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:19579800-19595800	Weak transcription	HUVEC	blood vessel
10	chr19:19579800-19598600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:19579800-19599200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:19579800-19599800	Weak transcription	Brain Substantia Nigra	brain
13	chr19:19580600-19595200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:19580600-19597200	Weak transcription	Brain Anterior Caudate	brain
15	chr19:19580800-19593600	Strong transcription	Fetal Intestine Small	intestine
16	chr19:19581400-19589000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:19581600-19595200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:19582200-19597600	Strong transcription	Dnd41	blood
19	chr19:19583400-19588000	Genic enhancers	Spleen	Spleen
20	chr19:19583400-19588400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr19:19583400-19588800	Genic enhancers	Primary T cells fromperipheralblood	blood
22	chr19:19583600-19588000	Genic enhancers	K562	blood
23	chr19:19583600-19588200	Strong transcription	Fetal Intestine Large	intestine
24	chr19:19583600-19588600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:19583600-19588800	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr19:19583600-19589200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:19583600-19593200	Weak transcription	Fetal Lung	lung
28	chr19:19584200-19588600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:19584200-19600000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:19584400-19588000	Strong transcription	Primary T cells from cord blood	blood
31	chr19:19584400-19589000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr19:19584400-19595600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:19584800-19588400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:19585200-19588200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:19585200-19589200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr19:19585200-19591000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr19:19585400-19588400	Enhancers	Primary hematopoietic stem cells	blood
38	chr19:19585400-19589200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:19585400-19591000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:19585400-19591200	Weak transcription	Aorta	Aorta
41	chr19:19585400-19596000	Weak transcription	HMEC	breast
42	chr19:19585600-19588200	Weak transcription	A549	lung
43	chr19:19585600-19589000	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr19:19585600-19594200	Weak transcription	NH-A	brain
45	chr19:19585800-19588000	Strong transcription	NHLF	lung
46	chr19:19585800-19588200	Strong transcription	Hela-S3	cervix
47	chr19:19585800-19588800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr19:19585800-19591200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:19586000-19588600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:19586200-19588200	Weak transcription	Gastric	stomach

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