Variant report

Variant	rs10403716
Chromosome Location	chr19:38658900-38658901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10401165	0.89[ASN][1000 genomes]
rs10405667	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10412762	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412865	0.97[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420506	0.93[ASN][1000 genomes]
rs10422665	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1568975	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1614979	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1622409	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1625884	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1654355	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1654357	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654358	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654359	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654365	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1654367	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1725461	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1725473	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1725479	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1725512	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2005054	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2082442	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082443	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28495744	0.85[ASN][1000 genomes]
rs28581256	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760882	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3810356	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4802233	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4802239	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4802247	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802256	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803786	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803800	0.87[EUR][1000 genomes]
rs4803801	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803802	0.87[EUR][1000 genomes]
rs4803803	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803809	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803810	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803828	0.95[ASN][1000 genomes]
rs4803829	0.93[ASN][1000 genomes]
rs56166457	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58152231	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59185302	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59579475	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59924887	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61388128	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508767	0.89[ASN][1000 genomes]
rs705505	0.87[EUR][1000 genomes]
rs71179415	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7245788	0.93[ASN][1000 genomes]
rs7248428	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7250034	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256332	0.85[ASN][1000 genomes]
rs729625	0.86[EUR][1000 genomes]
rs729626	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs735615	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73627654	0.93[ASN][1000 genomes]
rs73627663	0.93[ASN][1000 genomes]
rs73627676	0.93[ASN][1000 genomes]
rs73627686	0.84[ASN][1000 genomes]
rs73930553	0.83[ASN][1000 genomes]
rs754123	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8105468	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8106266	0.84[EUR][1000 genomes]
rs855619	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855621	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855623	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855624	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855625	0.82[EUR][1000 genomes]
rs855627	0.85[EUR][1000 genomes]
rs855630	0.86[EUR][1000 genomes]
rs855633	0.84[EUR][1000 genomes]
rs855634	0.84[EUR][1000 genomes]
rs855638	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855640	0.87[EUR][1000 genomes]
rs855641	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs860623	0.84[EUR][1000 genomes]
rs863020	0.85[EUR][1000 genomes]
rs941039	0.84[EUR][1000 genomes]
rs941040	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9941456	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941467	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10403716	SIPA1L3	cis	Heart Left Ventricle	GTEx
rs10403716	DPF1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:38644000-38659200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:38645600-38660800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:38646000-38661000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:38653400-38659600	Strong transcription	Primary B cells from cord blood	blood
6	chr19:38653400-38659600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr19:38653400-38660400	Strong transcription	GM12878-XiMat	blood
8	chr19:38653400-38661400	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr19:38653400-38663400	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:38653600-38659000	Weak transcription	Fetal Heart	heart
11	chr19:38653600-38659200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:38653600-38659600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr19:38653600-38659800	Weak transcription	Fetal Brain Male	brain
14	chr19:38653600-38660200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:38653600-38660200	Strong transcription	Primary T cells from cord blood	blood
16	chr19:38653600-38660400	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr19:38653600-38661200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:38653600-38661200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr19:38653600-38661400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr19:38653600-38661400	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr19:38653600-38661600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:38653600-38663200	Strong transcription	Gastric	stomach
23	chr19:38653600-38663400	Weak transcription	HUVEC	blood vessel
24	chr19:38653600-38663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:38653600-38663800	Strong transcription	Fetal Intestine Large	intestine
26	chr19:38653600-38665200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:38653600-38668600	Strong transcription	Primary B cells from peripheral blood	blood
28	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
29	chr19:38653800-38660400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:38653800-38660400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:38653800-38661600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr19:38653800-38661600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr19:38653800-38662400	Weak transcription	Brain Substantia Nigra	brain
34	chr19:38653800-38663600	Weak transcription	HMEC	breast
35	chr19:38653800-38663800	Strong transcription	Fetal Intestine Small	intestine
36	chr19:38653800-38664000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:38653800-38666600	Strong transcription	A549	lung
38	chr19:38653800-38670800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:38654000-38659200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:38654000-38663000	Weak transcription	NHEK	skin
41	chr19:38654000-38664000	Strong transcription	Fetal Stomach	stomach
42	chr19:38654200-38660200	Strong transcription	Adipose Nuclei	Adipose
43	chr19:38654200-38661000	Strong transcription	Liver	Liver
44	chr19:38654200-38661600	Strong transcription	Osteobl	bone
45	chr19:38654600-38659600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:38654800-38659800	Strong transcription	Spleen	Spleen
47	chr19:38655000-38661600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:38655200-38669400	Weak transcription	Fetal Lung	lung
49	chr19:38656000-38659200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr19:38656000-38659200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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