Variant report

Variant	rs4802278
Chromosome Location	chr19:38691281-38691282
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10401165	0.82[EUR][1000 genomes]
rs10412762	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs10420506	0.93[CEU][hapmap];0.90[CHB][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs10422665	0.81[CEU][hapmap]
rs1654365	0.81[CHB][hapmap]
rs28495744	0.83[EUR][1000 genomes]
rs4802256	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[TSI][hapmap]
rs4803828	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap]
rs4803829	0.93[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs4803862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6508767	0.81[EUR][1000 genomes]
rs7245788	0.81[EUR][1000 genomes]
rs7256332	0.83[EUR][1000 genomes]
rs73627654	0.80[EUR][1000 genomes]
rs73627663	0.82[EUR][1000 genomes]
rs73627676	0.82[EUR][1000 genomes]
rs73627686	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73930553	0.88[EUR][1000 genomes]
rs855633	0.81[CHB][hapmap]
rs860623	0.81[CHB][hapmap]
rs863020	0.81[CHB][hapmap]
rs941039	0.81[CHB][hapmap]
rs9941467	0.81[CEU][hapmap];0.90[CHB][hapmap]

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
rs4802278	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
2	chr19:38657600-38696200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:38658400-38694000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr19:38664600-38699800	Weak transcription	Brain Substantia Nigra	brain
5	chr19:38671200-38691800	Weak transcription	Brain Angular Gyrus	brain
6	chr19:38671800-38692400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr19:38671800-38695600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:38672200-38692800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr19:38672600-38699800	Weak transcription	HUVEC	blood vessel
10	chr19:38672800-38693400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:38674400-38696400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:38674600-38691600	Weak transcription	Psoas Muscle	Psoas
13	chr19:38674600-38696800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:38674600-38698600	Strong transcription	Fetal Intestine Small	intestine
15	chr19:38674800-38692200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:38674800-38692400	Weak transcription	Fetal Brain Male	brain
17	chr19:38674800-38696200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:38674800-38696800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr19:38674800-38697000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:38674800-38699000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:38674800-38699000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:38674800-38700400	Weak transcription	Fetal Kidney	kidney
23	chr19:38675000-38692800	Weak transcription	Fetal Lung	lung
24	chr19:38675400-38700200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:38675600-38691800	Weak transcription	Placenta	Placenta
26	chr19:38675600-38696800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:38675800-38694600	Weak transcription	Colon Smooth Muscle	Colon
28	chr19:38676000-38699800	Weak transcription	Right Atrium	heart
29	chr19:38676400-38693600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr19:38676800-38692000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:38676800-38692200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr19:38676800-38698200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:38679400-38699400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr19:38679600-38697800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr19:38679800-38698400	Strong transcription	Fetal Intestine Large	intestine
36	chr19:38679800-38698600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr19:38680000-38699400	Weak transcription	Dnd41	blood
38	chr19:38680600-38697800	Strong transcription	Fetal Stomach	stomach
39	chr19:38680600-38698000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:38680600-38698400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:38680600-38698600	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr19:38681000-38698200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:38681000-38698400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr19:38682200-38697800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr19:38682200-38698400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:38682400-38697800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr19:38682600-38694800	Strong transcription	Osteobl	bone
48	chr19:38682600-38695200	Strong transcription	Colonic Mucosa	Colon
49	chr19:38682600-38697000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr19:38682600-38697200	Strong transcription	Skeletal Muscle Female	skeletal muscle

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