Variant report

Variant	rs3760882
Chromosome Location	chr19:38591045-38591046
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10403716	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10405667	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10412865	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10422665	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1568975	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1614979	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1622409	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1625884	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654355	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1654357	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1654358	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654359	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1654365	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1654367	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1725461	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1725473	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1725479	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1725512	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2005054	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2082442	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2082443	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28412601	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28581256	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28587798	0.86[ASN][1000 genomes]
rs3810356	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802233	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802239	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4802247	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4803786	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4803800	0.87[EUR][1000 genomes]
rs4803801	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803802	0.87[EUR][1000 genomes]
rs4803803	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803809	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4803810	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56166457	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56293547	0.87[EUR][1000 genomes]
rs58152231	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59185302	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59579475	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59924887	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61388128	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs705505	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71179415	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7248428	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7250034	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs729625	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs729626	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs735615	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs754123	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8105468	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8106266	0.86[EUR][1000 genomes]
rs855597	0.84[ASN][1000 genomes]
rs855600	0.88[ASN][1000 genomes]
rs855601	0.88[ASN][1000 genomes]
rs855602	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs855603	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs855619	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs855621	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs855623	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs855624	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs855625	0.88[EUR][1000 genomes]
rs855627	0.91[EUR][1000 genomes]
rs855630	0.95[EUR][1000 genomes]
rs855631	0.84[EUR][1000 genomes]
rs855633	0.92[EUR][1000 genomes]
rs855634	0.92[EUR][1000 genomes]
rs855638	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs855640	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs855641	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs860623	0.90[EUR][1000 genomes]
rs863020	0.91[EUR][1000 genomes]
rs941039	0.92[EUR][1000 genomes]
rs941040	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9941456	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9941467	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[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
rs3760882	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
2	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr19:38567600-38605400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:38573600-38610000	Strong transcription	Fetal Intestine Large	intestine
5	chr19:38580400-38594800	Weak transcription	HSMMtube	muscle
6	chr19:38580600-38596000	Weak transcription	Stomach Mucosa	stomach
7	chr19:38581600-38610000	Weak transcription	Psoas Muscle	Psoas
8	chr19:38584400-38597000	Weak transcription	Right Atrium	heart
9	chr19:38584800-38602400	Weak transcription	Fetal Brain Male	brain
10	chr19:38584800-38602400	Weak transcription	Fetal Heart	heart
11	chr19:38586000-38592600	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr19:38587000-38605400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr19:38587200-38603200	Strong transcription	Primary B cells from cord blood	blood
14	chr19:38587200-38613600	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:38587400-38613400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr19:38588400-38593400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:38588600-38597200	Strong transcription	Osteobl	bone
18	chr19:38588600-38604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr19:38588800-38591600	ZNF genes & repeats	A549	lung
20	chr19:38588800-38606600	Strong transcription	Liver	Liver
21	chr19:38589200-38593000	Strong transcription	Colonic Mucosa	Colon
22	chr19:38589200-38606800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr19:38589400-38591600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:38589400-38592000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:38589400-38592800	Strong transcription	HepG2	liver
26	chr19:38589400-38593400	Strong transcription	Primary T cells from cord blood	blood
27	chr19:38589400-38595200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:38589800-38591200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:38590000-38591200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
30	chr19:38590000-38591200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:38590000-38591200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:38590000-38591200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr19:38590000-38591200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
34	chr19:38590000-38591200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
35	chr19:38590000-38591200	ZNF genes & repeats	Dnd41	blood
36	chr19:38590000-38591400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:38590000-38592800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr19:38590000-38593000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:38590000-38593400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr19:38590000-38593400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr19:38590000-38593800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:38590000-38594000	Strong transcription	Rectal Smooth Muscle	rectum
43	chr19:38590200-38591200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
44	chr19:38590200-38591200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
45	chr19:38590200-38591200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr19:38590200-38591200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:38590200-38591200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:38590200-38591200	Strong transcription	HUVEC	blood vessel
49	chr19:38590200-38591400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
50	chr19:38590200-38591600	ZNF genes & repeats	HMEC	breast

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