Variant report

Variant	rs10401165
Chromosome Location	chr19:38671201-38671202
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr19:38670700-38671217	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000269653	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10403716	0.89[ASN][1000 genomes]
rs10412762	0.89[ASN][1000 genomes]
rs10412865	0.89[ASN][1000 genomes]
rs10420506	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10422665	0.86[ASN][1000 genomes]
rs11083448	0.82[EUR][1000 genomes]
rs2082442	0.89[ASN][1000 genomes]
rs2082443	0.89[ASN][1000 genomes]
rs28444246	0.94[EUR][1000 genomes]
rs28495744	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28581256	0.85[ASN][1000 genomes]
rs4802247	0.87[ASN][1000 genomes]
rs4802256	0.89[ASN][1000 genomes]
rs4802278	0.82[EUR][1000 genomes]
rs4803786	0.82[ASN][1000 genomes]
rs4803809	0.89[ASN][1000 genomes]
rs4803810	0.89[ASN][1000 genomes]
rs4803828	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803829	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59185302	0.82[ASN][1000 genomes]
rs59924887	0.82[ASN][1000 genomes]
rs61388128	0.82[ASN][1000 genomes]
rs6508767	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245788	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7248428	0.85[ASN][1000 genomes]
rs7250034	0.89[ASN][1000 genomes]
rs7256332	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73627654	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73627663	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73627676	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73627686	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73930553	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105468	0.82[ASN][1000 genomes]
rs9941456	0.89[ASN][1000 genomes]
rs9941467	0.89[ASN][1000 genomes]

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	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
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10401165	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
2	chr19:38656200-38675200	Weak transcription	Stomach Mucosa	stomach
3	chr19:38656400-38671400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:38656400-38674000	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:38657600-38673400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:38657600-38673800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:38657600-38696200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:38658400-38674000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr19:38658400-38684800	Weak transcription	HepG2	liver
10	chr19:38658400-38694000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr19:38659600-38673600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr19:38659600-38673600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr19:38661000-38673200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:38661200-38673600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:38661400-38682600	Weak transcription	Aorta	Aorta
16	chr19:38661600-38671600	Weak transcription	Osteobl	bone
17	chr19:38661600-38673600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:38661600-38674000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:38661800-38682400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:38663200-38673200	Weak transcription	Gastric	stomach
21	chr19:38664400-38673200	Weak transcription	Colonic Mucosa	Colon
22	chr19:38664600-38674000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:38664600-38688600	Weak transcription	NH-A	brain
24	chr19:38664600-38699800	Weak transcription	Brain Substantia Nigra	brain
25	chr19:38664800-38673600	Weak transcription	Brain Anterior Caudate	brain
26	chr19:38664800-38674200	Weak transcription	Brain Hippocampus Middle	brain
27	chr19:38665000-38672800	Weak transcription	HSMMtube	muscle
28	chr19:38665000-38673200	Weak transcription	Esophagus	oesophagus
29	chr19:38665000-38684400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:38665200-38673200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:38665200-38674200	Weak transcription	Psoas Muscle	Psoas
32	chr19:38665200-38684200	Weak transcription	HMEC	breast
33	chr19:38666200-38682800	Weak transcription	Right Ventricle	heart
34	chr19:38666400-38671400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr19:38666400-38672800	Weak transcription	NHLF	lung
36	chr19:38666400-38673200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:38666400-38673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:38666400-38673400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:38666400-38673600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:38666600-38671400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:38667200-38673400	Weak transcription	NHEK	skin
42	chr19:38668400-38671600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr19:38668600-38671800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
44	chr19:38668600-38672000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:38668600-38672200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:38669200-38672000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:38669400-38671800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
48	chr19:38669400-38671800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:38669400-38671800	ZNF genes & repeats	Fetal Intestine Small	intestine
50	chr19:38669400-38672000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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