Variant report

Variant	rs1643466
Chromosome Location	chr19:38459654-38459655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38455932..38458635-chr19:38458979..38461344,2	MCF-7	breast:
2	chr19:38422859..38424594-chr19:38457914..38459896,2	MCF-7	breast:
3	chr19:38459331..38461760-chr19:38470604..38472306,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10404567	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs10415548	0.82[CEU][hapmap]
rs10420746	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs1119229	0.87[CEU][hapmap]
rs1643462	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1643463	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1643467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1643469	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725469	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725477	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1725478	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725480	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];0.81[JPT][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1725482	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1725483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725485	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1725487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725488	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1725494	0.92[EUR][1000 genomes]
rs1725499	0.82[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs2544718	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs35209753	0.83[EUR][1000 genomes]
rs353398	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353399	0.95[EUR][1000 genomes]
rs353400	0.95[EUR][1000 genomes]
rs353402	0.95[EUR][1000 genomes]
rs353403	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs353404	0.95[EUR][1000 genomes]
rs353407	0.95[EUR][1000 genomes]
rs353410	0.82[CEU][hapmap]
rs353411	0.82[CEU][hapmap]
rs353414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs353415	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs353416	0.95[EUR][1000 genomes]
rs353417	0.95[EUR][1000 genomes]
rs353419	0.95[EUR][1000 genomes]
rs353420	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353421	0.95[EUR][1000 genomes]
rs353423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353424	0.95[EUR][1000 genomes]
rs353425	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353426	0.93[EUR][1000 genomes]
rs353427	0.95[EUR][1000 genomes]
rs353428	0.91[EUR][1000 genomes]
rs353429	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs353430	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3786869	0.82[CEU][hapmap]
rs4239516	0.82[CEU][hapmap]
rs4802135	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs4803524	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs4803551	0.87[CEU][hapmap]
rs4803573	0.87[CEU][hapmap]
rs705491	0.87[CEU][hapmap]
rs705492	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs705493	0.87[CEU][hapmap]
rs705494	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs705495	0.87[CEU][hapmap]
rs705500	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7250409	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.86[EUR][1000 genomes]
rs7258597	0.85[EUR][1000 genomes]
rs752878	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs8107341	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs8113521	0.82[CEU][hapmap]
rs833895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs833896	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs833897	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs833898	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs833914	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs833926	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs856304	1.00[CEU][hapmap];0.80[CHB][hapmap]
rs9304572	0.86[EUR][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	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1643466	WDR87	cis	Thyroid	GTEx
rs1643466	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38454400-38460800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:38454400-38461200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr19:38454600-38460800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr19:38454600-38461000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr19:38455200-38461400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr19:38456000-38461000	Weak transcription	Fetal Stomach	stomach
7	chr19:38456600-38460800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr19:38457200-38461200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr19:38457200-38470400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:38457400-38460400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:38457400-38461000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:38457600-38460400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:38457600-38461000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:38457600-38461000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:38457600-38461200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr19:38457600-38461200	Weak transcription	NHDF-Ad	bronchial
17	chr19:38457600-38470200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:38457600-38470400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr19:38457600-38470400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:38457800-38460200	Weak transcription	Primary T cells from cord blood	blood
21	chr19:38457800-38460200	Weak transcription	Stomach Mucosa	stomach
22	chr19:38457800-38461000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:38457800-38461000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr19:38457800-38461000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr19:38457800-38461000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:38457800-38461000	Weak transcription	Spleen	Spleen
27	chr19:38457800-38461200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:38457800-38461200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:38457800-38461200	Weak transcription	Colonic Mucosa	Colon
30	chr19:38457800-38461200	Weak transcription	Gastric	stomach
31	chr19:38457800-38461400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr19:38457800-38468200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:38457800-38468400	Weak transcription	NH-A	brain
34	chr19:38458000-38460200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:38458000-38460200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:38458000-38460200	Weak transcription	NHEK	skin
37	chr19:38458000-38460800	Weak transcription	Primary B cells from cord blood	blood
38	chr19:38458000-38461000	Weak transcription	Fetal Intestine Large	intestine
39	chr19:38458000-38461000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr19:38458200-38461200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:38458200-38468600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:38458400-38461000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:38458400-38461000	Weak transcription	Osteobl	bone
44	chr19:38458400-38461200	Weak transcription	HepG2	liver
45	chr19:38458600-38460400	Weak transcription	HMEC	breast
46	chr19:38459000-38464800	ZNF genes & repeats	A549	lung
47	chr19:38459200-38463400	ZNF genes & repeats	GM12878-XiMat	blood
48	chr19:38459400-38460600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:38459400-38463800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:38459600-38460200	Weak transcription	Fetal Intestine Small	intestine

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