Variant report

Variant	rs9941456
Chromosome Location	chr19:38627816-38627817
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38626756..38629308-chr19:38639108..38640952,2	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10401165	0.89[ASN][1000 genomes]
rs10403716	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405667	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10412762	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412865	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413751	0.81[JPT][hapmap]
rs10420506	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10422665	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1568975	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1614979	0.81[CEU][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1622409	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1625884	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1654349	0.81[JPT][hapmap]
rs1654355	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1654357	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654358	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654359	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1654365	0.81[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1654367	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1725461	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1725473	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1725475	0.81[JPT][hapmap]
rs1725479	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1725512	0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2005054	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2010234	0.81[YRI][hapmap]
rs2082442	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082443	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28412601	0.86[AMR][1000 genomes]
rs28495744	0.85[ASN][1000 genomes]
rs28581256	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3760882	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3810356	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4802233	0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4802239	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4802247	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802256	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802278	0.90[CHB][hapmap]
rs4803786	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803800	0.98[EUR][1000 genomes]
rs4803801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803802	0.98[EUR][1000 genomes]
rs4803803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4803809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803810	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803828	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4803829	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4803862	0.90[CHB][hapmap]
rs56166457	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58152231	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59185302	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59579475	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59924887	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61388128	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6508767	0.89[ASN][1000 genomes]
rs705505	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71179415	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7245788	0.93[ASN][1000 genomes]
rs7248428	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7250034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256332	0.85[ASN][1000 genomes]
rs729625	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs729626	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs735615	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73627654	0.93[ASN][1000 genomes]
rs73627663	0.93[ASN][1000 genomes]
rs73627676	0.93[ASN][1000 genomes]
rs73627686	0.84[ASN][1000 genomes]
rs73930553	0.83[ASN][1000 genomes]
rs754123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8105468	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8106266	0.94[EUR][1000 genomes]
rs855601	0.81[JPT][hapmap]
rs855603	0.81[JPT][hapmap]
rs855619	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855621	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855623	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855624	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855625	0.88[EUR][1000 genomes]
rs855627	0.91[EUR][1000 genomes]
rs855630	0.86[EUR][1000 genomes]
rs855631	0.81[EUR][1000 genomes]
rs855633	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes]
rs855634	0.90[EUR][1000 genomes]
rs855636	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs855637	0.81[JPT][hapmap]
rs855638	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855640	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs855641	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs860623	0.87[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes]
rs863020	0.87[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs941039	0.87[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes]
rs941040	0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9941467	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv138463	chr19:38626819-38628763	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9941456	SIPA1L3	cis	Heart Left Ventricle	GTEx
rs9941456	DPF1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
2	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
3	chr19:38610800-38643600	Weak transcription	HepG2	liver
4	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:38611600-38634400	Weak transcription	Stomach Mucosa	stomach
6	chr19:38611600-38634800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr19:38611600-38634800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:38611600-38641400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:38611600-38653000	Weak transcription	HUVEC	blood vessel
10	chr19:38611800-38634600	Weak transcription	NH-A	brain
11	chr19:38611800-38642600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:38611800-38653000	Weak transcription	Fetal Kidney	kidney
13	chr19:38613400-38633600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:38613400-38634400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:38613600-38634800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr19:38613800-38629800	Weak transcription	Liver	Liver
17	chr19:38613800-38630000	Weak transcription	Brain Hippocampus Middle	brain
18	chr19:38613800-38633000	Weak transcription	Brain Angular Gyrus	brain
19	chr19:38613800-38633000	Weak transcription	Brain Substantia Nigra	brain
20	chr19:38613800-38633400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:38613800-38635600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr19:38613800-38636600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr19:38613800-38639000	Weak transcription	Left Ventricle	heart
24	chr19:38613800-38641800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:38613800-38643200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr19:38613800-38652200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:38613800-38652600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:38614000-38630200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:38614000-38634800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:38616000-38652600	Strong transcription	Primary B cells from peripheral blood	blood
31	chr19:38616200-38641600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr19:38616600-38642000	Weak transcription	Dnd41	blood
33	chr19:38617000-38652000	Strong transcription	Fetal Intestine Small	intestine
34	chr19:38618200-38651000	Strong transcription	Fetal Intestine Large	intestine
35	chr19:38619000-38630800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr19:38619600-38647800	Strong transcription	Fetal Stomach	stomach
37	chr19:38620800-38632600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:38621000-38633800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr19:38621400-38629000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:38621600-38630400	Weak transcription	Ovary	ovary
41	chr19:38621600-38642800	Weak transcription	NHLF	lung
42	chr19:38621800-38634000	Weak transcription	Thymus	Thymus
43	chr19:38622000-38634600	Weak transcription	Brain Germinal Matrix	brain
44	chr19:38622200-38636800	Weak transcription	Brain Anterior Caudate	brain
45	chr19:38622400-38634000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:38622600-38630200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:38622600-38641800	Weak transcription	Aorta	Aorta
48	chr19:38622800-38630000	Weak transcription	Gastric	stomach
49	chr19:38622800-38634000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr19:38622800-38634600	Weak transcription	Adipose Nuclei	Adipose

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