Variant report

Variant	rs59924887
Chromosome Location	chr19:38610542-38610543
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10401165	0.82[ASN][1000 genomes]
rs10403716	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10405667	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10412762	0.93[ASN][1000 genomes]
rs10412865	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10420506	0.87[ASN][1000 genomes]
rs10422665	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1568975	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1614979	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1622409	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1625884	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1654355	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1654357	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1654358	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1654359	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1654365	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1654367	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1725461	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1725473	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1725479	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1725512	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2005054	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2082442	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2082443	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28412601	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28581256	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760882	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3810356	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802233	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4802239	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4802247	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802256	0.93[ASN][1000 genomes]
rs4803786	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803800	0.92[EUR][1000 genomes]
rs4803801	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803802	0.92[EUR][1000 genomes]
rs4803803	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803809	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803810	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803828	0.88[ASN][1000 genomes]
rs4803829	0.87[ASN][1000 genomes]
rs56166457	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56293547	0.82[EUR][1000 genomes]
rs58152231	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59185302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59579475	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61388128	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508767	0.82[ASN][1000 genomes]
rs705505	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71179415	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7245788	0.87[ASN][1000 genomes]
rs7248428	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7250034	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs729625	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs729626	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs735615	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73627654	0.87[ASN][1000 genomes]
rs73627663	0.87[ASN][1000 genomes]
rs73627676	0.87[ASN][1000 genomes]
rs754123	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8105468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106266	0.91[EUR][1000 genomes]
rs855603	0.81[EUR][1000 genomes]
rs855619	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs855621	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs855623	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs855624	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs855625	0.93[EUR][1000 genomes]
rs855627	0.97[EUR][1000 genomes]
rs855630	0.91[EUR][1000 genomes]
rs855631	0.87[EUR][1000 genomes]
rs855633	0.96[EUR][1000 genomes]
rs855634	0.96[EUR][1000 genomes]
rs855638	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs855640	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs855641	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs860623	0.96[EUR][1000 genomes]
rs863020	0.97[EUR][1000 genomes]
rs941039	0.96[EUR][1000 genomes]
rs941040	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9941456	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9941467	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][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
rs59924887	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr19:38587200-38613600	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr19:38587400-38613400	Strong transcription	Duodenum Mucosa	Duodenum
4	chr19:38590200-38611000	Strong transcription	Duodenum Smooth Muscle	Duodenum
5	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
6	chr19:38596000-38613800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:38597800-38611800	Strong transcription	Osteobl	bone
8	chr19:38597800-38612000	Strong transcription	HSMM	muscle
9	chr19:38598200-38611800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
11	chr19:38602800-38612800	Weak transcription	Hela-S3	cervix
12	chr19:38603000-38611200	Weak transcription	Fetal Brain Male	brain
13	chr19:38603000-38625400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:38603200-38611200	Weak transcription	Fetal Heart	heart
15	chr19:38604000-38613400	Strong transcription	Primary B cells from cord blood	blood
16	chr19:38605800-38625400	Weak transcription	HMEC	breast
17	chr19:38606000-38613000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr19:38606200-38612000	Strong transcription	Primary B cells from peripheral blood	blood
19	chr19:38606200-38612800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr19:38606200-38613800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:38607200-38613800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:38607600-38613200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr19:38607600-38613400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:38607600-38613800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:38607600-38613800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:38607800-38613800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:38608000-38610600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr19:38608200-38611600	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr19:38608400-38611200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr19:38608400-38611600	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr19:38608400-38611600	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:38608400-38611800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:38608400-38613800	Strong transcription	Liver	Liver
34	chr19:38608600-38612000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:38608800-38611200	Strong transcription	Adipose Nuclei	Adipose
36	chr19:38608800-38611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr19:38608800-38613600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:38608800-38614000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:38608800-38614000	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr19:38609000-38611200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr19:38609000-38611800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:38609000-38611800	ZNF genes & repeats	Fetal Stomach	stomach
43	chr19:38609000-38611800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:38609200-38611200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:38609200-38611800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
46	chr19:38609400-38611000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr19:38609400-38611600	Strong transcription	Rectal Smooth Muscle	rectum
48	chr19:38609400-38611800	Strong transcription	Primary T cells from cord blood	blood
49	chr19:38609400-38611800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:38609400-38611800	Strong transcription	Brain Hippocampus Middle	brain

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