Variant report

Variant	rs1725512
Chromosome Location	chr19:38571728-38571729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38504278..38506412-chr19:38570707..38572252,2	MCF-7	breast:
2	chr19:38395477..38398410-chr19:38570467..38573165,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10403716	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10405667	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10412762	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs10413751	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10414433	0.83[CEU][hapmap]
rs10420506	0.81[JPT][hapmap]
rs10422665	0.82[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes]
rs1568975	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1614979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1622409	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1625884	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1654349	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1654355	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1654357	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1654358	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1654359	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1654365	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1654367	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1725461	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725473	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1725475	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1725479	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2005054	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2082442	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2082443	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28412601	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28581256	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3760882	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3810356	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4802233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802239	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4802247	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4802256	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4803786	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803800	0.82[EUR][1000 genomes]
rs4803801	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4803802	0.82[EUR][1000 genomes]
rs4803803	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4803809	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4803810	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4803828	0.81[JPT][hapmap]
rs4803829	0.81[JPT][hapmap]
rs56166457	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56293547	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58152231	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59185302	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59579475	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59924887	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61388128	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs705505	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71179415	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7248428	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7250034	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs729625	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs729626	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs735615	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs754123	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8105468	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8106266	0.81[EUR][1000 genomes]
rs855598	0.84[ASN][1000 genomes]
rs855599	0.83[ASN][1000 genomes]
rs855601	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs855602	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs855603	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs855619	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs855621	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs855623	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs855624	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs855625	0.81[EUR][1000 genomes]
rs855627	0.84[EUR][1000 genomes]
rs855630	0.87[EUR][1000 genomes]
rs855633	0.94[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs855634	0.85[EUR][1000 genomes]
rs855636	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs855637	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs855638	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs855640	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs855641	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs860623	0.94[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs863020	0.94[CEU][hapmap];0.83[CHB][hapmap];0.84[EUR][1000 genomes]
rs941039	0.94[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs941040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9941456	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9941467	0.87[CEU][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1725512	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
2	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
3	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
4	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr19:38549200-38572000	Weak transcription	Liver	Liver
6	chr19:38549600-38572600	Weak transcription	Thymus	Thymus
7	chr19:38550800-38572200	Weak transcription	Colonic Mucosa	Colon
8	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr19:38551000-38572000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr19:38553800-38572000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:38554200-38572600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:38554600-38571800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr19:38554800-38571800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:38554800-38573200	Weak transcription	Brain Angular Gyrus	brain
16	chr19:38554800-38580200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:38564000-38572400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr19:38564200-38571800	Weak transcription	Primary T cells from cord blood	blood
19	chr19:38564200-38571800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr19:38564600-38572000	Weak transcription	Fetal Brain Female	brain
21	chr19:38564800-38579000	Weak transcription	Fetal Lung	lung
22	chr19:38565000-38579200	Weak transcription	Brain Substantia Nigra	brain
23	chr19:38565200-38572200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:38565200-38572400	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:38565400-38571800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr19:38565600-38572200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:38565600-38572800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr19:38565600-38588400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:38565800-38572400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr19:38567200-38572000	Weak transcription	Brain Germinal Matrix	brain
31	chr19:38567200-38572000	Weak transcription	Ovary	ovary
32	chr19:38567400-38571800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:38567400-38571800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:38567600-38573200	Weak transcription	Brain Anterior Caudate	brain
35	chr19:38567600-38605400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:38567800-38571800	Weak transcription	Aorta	Aorta
37	chr19:38567800-38572000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr19:38567800-38573000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr19:38568000-38590200	Strong transcription	Fetal Intestine Small	intestine
40	chr19:38568600-38572000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr19:38569000-38571800	Weak transcription	Fetal Stomach	stomach
42	chr19:38569000-38573400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr19:38569200-38572200	Enhancers	NHDF-Ad	bronchial
44	chr19:38569400-38571800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:38569400-38572200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:38569600-38572600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:38569800-38571800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr19:38569800-38572000	Weak transcription	Dnd41	blood
49	chr19:38570000-38571800	Enhancers	Primary B cells from peripheral blood	blood
50	chr19:38570000-38571800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links