Variant report

Variant	rs1614979
Chromosome Location	chr19:38577437-38577438
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10403716	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10405667	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10412762	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs10413751	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10414433	0.82[CEU][hapmap]
rs10420506	0.81[JPT][hapmap]
rs10422665	0.87[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1568975	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1622409	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];0.81[ASN][1000 genomes]
rs1654349	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1654355	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654358	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1654359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654365	0.81[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654367	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1725473	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1725475	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1725479	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725506	0.80[ASN][1000 genomes]
rs1725512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[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	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3810356	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802239	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802247	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4802256	0.87[CEU][hapmap];0.94[GIH][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	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56293547	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58152231	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59185302	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59579475	0.82[AFR][1000 genomes];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];1.00[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];0.96[ASN][1000 genomes]
rs729626	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs735615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.89[ASN][1000 genomes]
rs855599	0.88[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];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs855619	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs855621	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs855623	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855624	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[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];0.83[CHB][hapmap];0.90[EUR][1000 genomes]
rs855634	0.90[EUR][1000 genomes]
rs855636	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs855637	0.82[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs855638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855640	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855641	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs860623	0.94[CEU][hapmap];0.83[CHB][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs863020	0.94[CEU][hapmap];0.83[CHB][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs941039	0.94[CEU][hapmap];0.83[CHB][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs941040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941456	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9941467	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.89[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
rs1614979	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:118 , 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	chr19:38550800-38590000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:38551200-38613800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:38554800-38580200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr19:38564800-38579000	Weak transcription	Fetal Lung	lung
6	chr19:38565000-38579200	Weak transcription	Brain Substantia Nigra	brain
7	chr19:38565600-38588400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:38567600-38605400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:38568000-38590200	Strong transcription	Fetal Intestine Small	intestine
10	chr19:38570600-38579000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr19:38570800-38584000	Weak transcription	Right Atrium	heart
12	chr19:38570800-38590200	Weak transcription	Fetal Thymus	thymus
13	chr19:38571000-38580800	Weak transcription	Hela-S3	cervix
14	chr19:38571000-38590000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:38571000-38590200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:38571200-38578800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr19:38571200-38579400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:38571200-38580000	Weak transcription	HSMMtube	muscle
19	chr19:38571200-38580200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr19:38571200-38590200	Weak transcription	HMEC	breast
21	chr19:38571200-38590200	Weak transcription	NHEK	skin
22	chr19:38571400-38579200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:38571400-38579200	Weak transcription	HepG2	liver
24	chr19:38571400-38586000	Strong transcription	A549	lung
25	chr19:38571600-38579200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr19:38571800-38582600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:38571800-38585000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr19:38571800-38585400	Strong transcription	Fetal Stomach	stomach
29	chr19:38571800-38586000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:38571800-38586600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:38572000-38585800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr19:38572000-38586000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr19:38572200-38579000	Weak transcription	NH-A	brain
34	chr19:38572200-38585800	Weak transcription	NHDF-Ad	bronchial
35	chr19:38572400-38579400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:38572400-38581400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:38573600-38586000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:38573600-38590000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr19:38573600-38610000	Strong transcription	Fetal Intestine Large	intestine
40	chr19:38573800-38578600	Weak transcription	Ovary	ovary
41	chr19:38573800-38579000	Weak transcription	Colonic Mucosa	Colon
42	chr19:38573800-38579200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr19:38573800-38584000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:38574000-38577800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr19:38574000-38578800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:38574000-38578800	Weak transcription	Brain Hippocampus Middle	brain
47	chr19:38574000-38578800	Weak transcription	Gastric	stomach
48	chr19:38574000-38578800	Weak transcription	Spleen	Spleen
49	chr19:38574000-38579000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:38574000-38579000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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