Variant report

Variant	rs12579616
Chromosome Location	chr12:30775978-30775979
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	chr12:30772709..30774221-chr12:30775456..30778099,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10444423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10743729	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10771745	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771756	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771757	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771762	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10771768	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs10843804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843813	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843814	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843815	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10843816	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10843817	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10843822	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs10843824	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs10843833	0.90[JPT][hapmap]
rs10843834	0.81[EUR][1000 genomes]
rs10843835	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs11051005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051008	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051010	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11051027	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051048	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051050	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs11051053	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs11051061	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs12146709	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12303852	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs12369125	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12370947	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12580645	0.88[AMR][1000 genomes]
rs12581001	0.88[AMR][1000 genomes]
rs12809335	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12809355	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12819059	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12825440	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12826615	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12829890	0.89[AMR][1000 genomes]
rs12830910	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2241828	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278558	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2289302	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304630	0.89[JPT][hapmap]
rs28824537	0.82[AFR][1000 genomes]
rs28881332	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34973510	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35133495	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36074842	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3933852	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4082413	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs4335626	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59177896	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61923728	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6487928	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6487939	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs7304221	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs7311530	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7314823	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7952744	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs7955804	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7957141	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs7966063	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7971762	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs7971870	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs7978343	0.88[CEU][hapmap]
rs7979718	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12579616	IPO8	Cis_1M	lymphoblastoid	RTeQTL
rs12579616	IPO8	cis	Artery Tibial	GTEx
rs12579616	IPO8	cis	multi-tissue	Pritchard

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30767000-30780800	Weak transcription	Fetal Muscle Leg	muscle
2	chr12:30767000-30784800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:30767000-30785600	Weak transcription	Pancreas	Pancrea
4	chr12:30767000-30844200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:30767600-30780800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:30767600-30780800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:30770600-30783400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:30770800-30783200	Weak transcription	Fetal Stomach	stomach
9	chr12:30771000-30781600	Weak transcription	Fetal Brain Female	brain
10	chr12:30771000-30812200	Weak transcription	Aorta	Aorta
11	chr12:30771200-30804200	Weak transcription	Fetal Brain Male	brain
12	chr12:30771400-30781200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:30771400-30783000	Weak transcription	Brain Germinal Matrix	brain
14	chr12:30771400-30783000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:30771400-30783000	Weak transcription	HSMMtube	muscle
16	chr12:30772800-30777000	Weak transcription	Lung	lung
17	chr12:30772800-30783400	Weak transcription	A549	lung
18	chr12:30774000-30780800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:30774200-30781200	Weak transcription	Brain Substantia Nigra	brain
20	chr12:30774400-30780800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:30774600-30812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:30775000-30781200	Weak transcription	Primary B cells from cord blood	blood
23	chr12:30775000-30781200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:30775000-30781600	Weak transcription	HUVEC	blood vessel
25	chr12:30775200-30776200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:30775200-30780600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:30775200-30783400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:30775400-30776000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:30775400-30776000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:30775400-30776000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr12:30775400-30776000	Enhancers	NHDF-Ad	bronchial
32	chr12:30775400-30781200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:30775600-30776000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:30775600-30776000	Strong transcription	Primary T cells from cord blood	blood
35	chr12:30775600-30776200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:30775600-30780800	Weak transcription	Esophagus	oesophagus
37	chr12:30775600-30780800	Weak transcription	Osteobl	bone
38	chr12:30775600-30781200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr12:30775600-30781200	Weak transcription	NHLF	lung
40	chr12:30775600-30781400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr12:30775600-30781600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:30775600-30815400	Weak transcription	Right Ventricle	heart
43	chr12:30775800-30776000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:30775800-30779400	Weak transcription	HepG2	liver
45	chr12:30775800-30780600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr12:30775800-30781200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:30775800-30781200	Weak transcription	Adipose Nuclei	Adipose
48	chr12:30775800-30783000	Weak transcription	HSMM	muscle
49	chr12:30775800-30784800	Weak transcription	GM12878-XiMat	blood
50	chr12:30775800-30813200	Weak transcription	HMEC	breast

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