Variant report

Variant	rs1725468
Chromosome Location	chr19:38473929-38473930
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38472838..38474664-chr19:38494090..38496793,2	MCF-7	breast:
2	chr19:38472927..38474902-chr19:38482178..38484229,2	K562	blood:
3	chr19:38470130..38474074-chr19:38479565..38484723,5	MCF-7	breast:
4	chr19:38473416..38476574-chr19:38478709..38480543,3	MCF-7	breast:
5	chr19:38469123..38470666-chr19:38472308..38474390,3	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10422056	0.84[AFR][1000 genomes]
rs11083439	0.84[AFR][1000 genomes]
rs11668384	0.84[AFR][1000 genomes]
rs12610891	0.84[AFR][1000 genomes]
rs1632177	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1643464	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1643465	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1643470	1.00[ASW][hapmap];0.80[CEU][hapmap];0.95[GIH][hapmap];0.96[MKK][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1643472	0.84[EUR][1000 genomes]
rs1725490	0.83[EUR][1000 genomes]
rs241937	1.00[ASW][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap]
rs241940	1.00[ASW][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap]
rs241942	1.00[ASW][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap]
rs353405	0.82[EUR][1000 genomes]
rs353406	0.85[EUR][1000 genomes]
rs353409	0.85[EUR][1000 genomes]
rs353412	0.85[EUR][1000 genomes]
rs353413	0.85[EUR][1000 genomes]
rs3894129	1.00[ASW][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs4803536	0.84[AFR][1000 genomes]
rs4803566	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6508748	0.84[AFR][1000 genomes]
rs6508752	0.80[EUR][1000 genomes]
rs697433	0.82[EUR][1000 genomes]
rs7250668	0.84[AFR][1000 genomes]
rs8102871	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs8103882	0.84[AFR][1000 genomes]
rs8105694	0.84[AFR][1000 genomes]
rs8110417	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs8111400	0.81[EUR][1000 genomes]
rs833915	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs833916	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs861308	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1725468	CEACAM16	cis	parietal	SCAN
rs1725468	LGALS4	cis	multi-tissue	Pritchard
rs1725468	TMEM145	cis	parietal	SCAN
rs1725468	CD3EAP	cis	cerebellum	SCAN
rs1725468	GSK3A	cis	parietal	SCAN
rs1725468	PPP5C	cis	parietal	SCAN
rs1725468	ARHGEF1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38461600-38476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:38461800-38476800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:38463600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
8	chr19:38466000-38475800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:38468200-38474200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:38468200-38474600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:38468200-38475600	Enhancers	HMEC	breast
12	chr19:38468200-38475800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:38468200-38483600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr19:38468800-38474000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:38469000-38474200	Enhancers	Fetal Intestine Large	intestine
16	chr19:38469200-38474800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:38469200-38479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:38469800-38475800	Genic enhancers	Fetal Intestine Small	intestine
19	chr19:38470200-38474200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr19:38470200-38474200	Enhancers	Stomach Mucosa	stomach
21	chr19:38470200-38474400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr19:38470400-38474400	Enhancers	Esophagus	oesophagus
23	chr19:38470400-38474800	Enhancers	Gastric	stomach
24	chr19:38470600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:38470800-38474600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr19:38470800-38477200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:38470800-38494000	Weak transcription	Right Ventricle	heart
28	chr19:38471000-38475400	Enhancers	NHEK	skin
29	chr19:38471000-38476800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:38471200-38474600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:38471200-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr19:38471400-38476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:38471400-38477000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:38471400-38483600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:38471400-38488600	Weak transcription	NHLF	lung
36	chr19:38471600-38476400	Weak transcription	Fetal Thymus	thymus
37	chr19:38471600-38477000	Weak transcription	Fetal Muscle Leg	muscle
38	chr19:38471800-38474000	Weak transcription	Brain Hippocampus Middle	brain
39	chr19:38471800-38474000	Weak transcription	Brain Substantia Nigra	brain
40	chr19:38471800-38474000	Genic enhancers	GM12878-XiMat	blood
41	chr19:38471800-38474200	Weak transcription	Brain Anterior Caudate	brain
42	chr19:38471800-38475400	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr19:38472000-38474200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:38472000-38476400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:38472200-38474200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:38472200-38474200	Enhancers	Colonic Mucosa	Colon
47	chr19:38472200-38474400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:38472200-38481200	Weak transcription	NHDF-Ad	bronchial
49	chr19:38472400-38474000	Weak transcription	Brain Angular Gyrus	brain
50	chr19:38472400-38474000	Genic enhancers	A549	lung

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