Variant report

Variant	rs1622409
Chromosome Location	chr19:38563632-38563633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10403716	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10405667	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10412762	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs10413751	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10414433	0.83[CEU][hapmap]
rs10420506	0.81[JPT][hapmap]
rs10422665	0.82[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1568975	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1614979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1625884	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1654349	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1654355	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1654357	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1654358	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1654359	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1654365	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1654367	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725461	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725473	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1725475	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1725479	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1725506	0.84[ASN][1000 genomes]
rs1725507	0.81[ASN][1000 genomes]
rs1725512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2005054	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2082442	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2082443	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28412601	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28581256	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3760882	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3810356	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4802233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4802239	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802247	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4802256	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4803786	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4803800	0.85[EUR][1000 genomes]
rs4803801	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803802	0.85[EUR][1000 genomes]
rs4803803	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803809	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803810	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4803828	0.81[JPT][hapmap]
rs4803829	0.81[JPT][hapmap]
rs56166457	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56293547	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58152231	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59185302	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59579475	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59924887	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61388128	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs705505	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71179415	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7248428	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7250034	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs729625	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729626	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs735615	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs754123	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8105468	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8106266	0.84[EUR][1000 genomes]
rs855598	0.92[ASN][1000 genomes]
rs855599	0.91[ASN][1000 genomes]
rs855601	0.83[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs855602	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs855603	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs855619	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855621	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855623	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855624	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs855625	0.86[EUR][1000 genomes]
rs855627	0.89[EUR][1000 genomes]
rs855630	0.92[EUR][1000 genomes]
rs855631	0.82[EUR][1000 genomes]
rs855633	0.94[CEU][hapmap];0.84[CHB][hapmap];0.90[EUR][1000 genomes]
rs855634	0.90[EUR][1000 genomes]
rs855636	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs855637	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs855638	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855640	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855641	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs860623	0.94[CEU][hapmap];0.83[CHB][hapmap];0.88[EUR][1000 genomes]
rs863020	0.94[CEU][hapmap];0.83[CHB][hapmap];0.89[EUR][1000 genomes]
rs941039	0.94[CEU][hapmap];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs941040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9941456	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9941467	0.87[CEU][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv1062518	chr19:38540454-38564913	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1622409	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38528200-38573200	Weak transcription	Left Ventricle	heart
2	chr19:38539000-38572000	Weak transcription	Right Ventricle	heart
3	chr19:38539200-38591200	Weak transcription	Small Intestine	intestine
4	chr19:38546600-38572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr19:38549200-38564800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr19:38549200-38572000	Weak transcription	Liver	Liver
7	chr19:38549600-38572600	Weak transcription	Thymus	Thymus
8	chr19:38550000-38570400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:38550800-38565200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr19:38550800-38570000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr19:38550800-38572200	Weak transcription	Colonic Mucosa	Colon
12	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:38551000-38572000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:38551200-38567000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr19:38551400-38567000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:38553200-38570400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:38553800-38572000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:38554200-38572600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:38554400-38564600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:38554600-38567000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr19:38554600-38570400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:38554600-38571800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr19:38554800-38571800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr19:38554800-38573200	Weak transcription	Brain Angular Gyrus	brain
26	chr19:38554800-38580200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr19:38555000-38570800	Weak transcription	Fetal Intestine Large	intestine
28	chr19:38561200-38570800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr19:38561400-38564600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr19:38561400-38570400	Weak transcription	Hela-S3	cervix
31	chr19:38561600-38564600	Weak transcription	HepG2	liver
32	chr19:38561600-38565400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:38561600-38567200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:38561600-38570000	Weak transcription	NHLF	lung
35	chr19:38561600-38570000	Weak transcription	Osteobl	bone
36	chr19:38561600-38570600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:38561800-38567000	Weak transcription	Pancreas	Pancrea
38	chr19:38561800-38570000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr19:38561800-38570200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:38561800-38570200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:38561800-38570400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr19:38561800-38570400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:38561800-38570400	Weak transcription	Esophagus	oesophagus
44	chr19:38561800-38570400	Weak transcription	Lung	lung
45	chr19:38561800-38570400	Weak transcription	HMEC	breast
46	chr19:38561800-38570400	Weak transcription	NHEK	skin
47	chr19:38562200-38564200	Strong transcription	Primary T cells from cord blood	blood
48	chr19:38562200-38564800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr19:38562200-38565600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:38562400-38565000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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