Variant report

Variant	rs2278558
Chromosome Location	chr12:30783743-30783744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:30776811..30779665-chr12:30781833..30784951,3	K562	blood:
2	chr12:29503193..29506083-chr12:30783016..30785826,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10444423	0.94[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs1054426	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10743727	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10743728	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10743729	0.94[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10771745	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10771746	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771747	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10771748	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10771750	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10771752	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10771754	0.90[JPT][hapmap]
rs10771755	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs10771756	0.81[EUR][1000 genomes]
rs10771757	0.80[EUR][1000 genomes]
rs10771762	0.82[EUR][1000 genomes]
rs10771764	0.90[JPT][hapmap]
rs10843796	0.87[CHB][hapmap]
rs10843799	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10843804	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs10843809	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10843810	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10843811	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10843812	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10843813	0.89[EUR][1000 genomes]
rs10843814	0.86[EUR][1000 genomes]
rs10843815	0.83[EUR][1000 genomes]
rs10843816	0.88[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs10843817	0.88[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs11051005	0.94[CEU][hapmap];0.96[GIH][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11051008	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11051010	0.90[EUR][1000 genomes]
rs11051013	0.90[JPT][hapmap]
rs11051027	0.86[EUR][1000 genomes]
rs11051048	0.82[EUR][1000 genomes]
rs11051050	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs11051052	0.86[JPT][hapmap]
rs12146709	0.88[CEU][hapmap];0.96[GIH][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs12369125	0.88[EUR][1000 genomes]
rs12370947	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12579616	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1258276	0.83[ASN][1000 genomes]
rs12809335	0.88[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12809355	0.86[EUR][1000 genomes]
rs12819059	0.83[AMR][1000 genomes]
rs12825440	0.90[EUR][1000 genomes]
rs12826615	0.90[EUR][1000 genomes]
rs12829890	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12830910	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs13656	0.85[JPT][hapmap]
rs1371053	0.95[JPT][hapmap]
rs14139	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1545175	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2043846	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2241828	0.85[EUR][1000 genomes]
rs2289300	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs2289301	0.90[JPT][hapmap]
rs2289302	0.94[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs28881332	0.81[AMR][1000 genomes]
rs33132	0.90[JPT][hapmap]
rs35133495	0.84[EUR][1000 genomes]
rs36074842	0.84[EUR][1000 genomes]
rs3782685	0.90[JPT][hapmap]
rs3825307	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3910561	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs3910564	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs4143104	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4143105	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs4335626	0.89[EUR][1000 genomes]
rs59177896	0.90[EUR][1000 genomes]
rs61923728	0.83[EUR][1000 genomes]
rs6487925	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs6487927	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs6487928	0.89[EUR][1000 genomes]
rs6487930	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs6487932	0.90[JPT][hapmap]
rs7297455	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7298007	0.85[JPT][hapmap]
rs7315693	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7316477	0.89[JPT][hapmap]
rs7325	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs7326	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs7327	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs794152	0.90[JPT][hapmap]
rs7955420	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7955804	0.90[EUR][1000 genomes]
rs7963494	0.90[JPT][hapmap]
rs7966063	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs7968343	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs7978343	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7979718	0.89[EUR][1000 genomes]
rs7980510	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs8414	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs9300199	0.90[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	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2278558	IPO8	cis	cerebellum	SCAN
rs2278558	IPO8	Cis_1M	lymphoblastoid	RTeQTL
rs2278558	IPO8	cis	multi-tissue	Pritchard
rs2278558	IPO8	cis	Artery Tibial	GTEx
rs2278558	IPO8	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30767000-30784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:30767000-30785600	Weak transcription	Pancreas	Pancrea
3	chr12:30767000-30844200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:30771000-30812200	Weak transcription	Aorta	Aorta
5	chr12:30771200-30804200	Weak transcription	Fetal Brain Male	brain
6	chr12:30774600-30812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:30775600-30815400	Weak transcription	Right Ventricle	heart
8	chr12:30775800-30784800	Weak transcription	GM12878-XiMat	blood
9	chr12:30775800-30813200	Weak transcription	HMEC	breast
10	chr12:30775800-30815200	Weak transcription	NHEK	skin
11	chr12:30776000-30808400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:30776800-30791000	Weak transcription	Psoas Muscle	Psoas
13	chr12:30778000-30786400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:30779200-30812200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:30779400-30796400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:30779800-30825000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr12:30780200-30795000	Weak transcription	Fetal Intestine Small	intestine
18	chr12:30780400-30796200	Weak transcription	Hela-S3	cervix
19	chr12:30780600-30785800	Strong transcription	Stomach Smooth Muscle	stomach
20	chr12:30780600-30788400	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:30780800-30784800	Strong transcription	Osteobl	bone
22	chr12:30780800-30786000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:30780800-30786000	Strong transcription	Fetal Muscle Leg	muscle
24	chr12:30780800-30786200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:30780800-30792600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:30780800-30793000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:30780800-30793000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:30780800-30793200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr12:30780800-30793200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr12:30780800-30847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:30781000-30787200	Strong transcription	Fetal Intestine Large	intestine
32	chr12:30781000-30792800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:30781000-30792800	Strong transcription	Primary T cells from cord blood	blood
34	chr12:30781000-30793000	Strong transcription	Liver	Liver
35	chr12:30781200-30783800	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr12:30781200-30784800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:30781200-30785200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:30781200-30786000	Strong transcription	Left Ventricle	heart
39	chr12:30781200-30786400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:30781200-30786800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:30781200-30787200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr12:30781200-30787200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:30781200-30787200	Strong transcription	Rectal Smooth Muscle	rectum
44	chr12:30781200-30787200	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:30781200-30790000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:30781200-30790200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr12:30781200-30792800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:30781200-30792800	Strong transcription	Primary B cells from peripheral blood	blood
49	chr12:30781200-30792800	Strong transcription	Adipose Nuclei	Adipose
50	chr12:30781200-30792800	Strong transcription	Rectal Mucosa Donor 29	rectum

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