Variant report

Variant	rs12462587
Chromosome Location	chr19:38587463-38587464
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:38587400-38587550	GM12873	blood:	n/a	n/a

Variant related genes	Relation type
SIPA1L3	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12459984	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12460013	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12461387	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12461946	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12971962	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12974504	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12979004	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12981412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12982030	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12982734	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12983059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12983497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12985707	0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1962866	0.82[ASN][1000 genomes]
rs2304132	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs2382972	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2382973	0.90[ASN][1000 genomes]
rs332857	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs332863	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[MKK][hapmap]
rs35469521	0.82[ASN][1000 genomes]
rs3745943	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3852910	0.83[ASN][1000 genomes]
rs3852911	0.89[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4802230	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803747	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7249265	0.81[JPT][hapmap]
rs7253312	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7253633	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs8102589	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107385	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12462587	LIPE	cis	cerebellum	SCAN
rs12462587	NANOS2	cis	parietal	SCAN
rs12462587	PAPL	cis	cerebellum	SCAN
rs12462587	LOC390940	cis	parietal	SCAN
rs12462587	PSG4	cis	cerebellum	SCAN
rs12462587	DEDD2	cis	cerebellum	SCAN

Chromatin state (count:123 , 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	chr19:38565600-38588400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:38567600-38605400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr19:38568000-38590200	Strong transcription	Fetal Intestine Small	intestine
7	chr19:38570800-38590200	Weak transcription	Fetal Thymus	thymus
8	chr19:38571000-38590000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:38571000-38590200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:38571200-38590200	Weak transcription	HMEC	breast
11	chr19:38571200-38590200	Weak transcription	NHEK	skin
12	chr19:38573600-38590000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr19:38573600-38610000	Strong transcription	Fetal Intestine Large	intestine
14	chr19:38574000-38590000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:38574000-38590200	Weak transcription	Aorta	Aorta
16	chr19:38574000-38590600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:38574200-38589600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:38574200-38590200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr19:38574200-38590200	Weak transcription	HUVEC	blood vessel
20	chr19:38574400-38590000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:38576400-38590000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr19:38579600-38590400	Weak transcription	Esophagus	oesophagus
23	chr19:38579800-38590200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr19:38579800-38590200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:38580000-38590600	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:38580200-38590000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:38580400-38590400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr19:38580400-38594800	Weak transcription	HSMMtube	muscle
29	chr19:38580600-38588000	Weak transcription	NH-A	brain
30	chr19:38580600-38588600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr19:38580600-38588600	Weak transcription	HSMM	muscle
32	chr19:38580600-38590000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:38580600-38590000	Weak transcription	Dnd41	blood
34	chr19:38580600-38590200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:38580600-38590200	Weak transcription	Fetal Lung	lung
36	chr19:38580600-38590200	Weak transcription	Ovary	ovary
37	chr19:38580600-38590200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr19:38580600-38590400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr19:38580600-38590600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:38580600-38596000	Weak transcription	Stomach Mucosa	stomach
41	chr19:38580800-38590200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr19:38581200-38589400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:38581600-38588800	Weak transcription	Liver	Liver
44	chr19:38581600-38590200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr19:38581600-38610000	Weak transcription	Psoas Muscle	Psoas
46	chr19:38581800-38588600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:38581800-38590200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr19:38581800-38590200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr19:38581800-38590200	Weak transcription	Gastric	stomach
50	chr19:38581800-38590400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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