Variant report

Variant	rs6487928
Chromosome Location	chr12:30828095-30828096
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10444423	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10734793	0.85[ASN][1000 genomes]
rs10743729	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10771745	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10771756	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10771757	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771760	0.86[ASN][1000 genomes]
rs10771761	0.86[ASN][1000 genomes]
rs10771762	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843804	0.89[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843813	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843814	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843815	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843816	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843817	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843818	0.86[ASN][1000 genomes]
rs10843819	0.86[ASN][1000 genomes]
rs10843820	0.86[ASN][1000 genomes]
rs10843821	0.86[ASN][1000 genomes]
rs10843822	0.86[ASN][1000 genomes]
rs10843823	0.86[ASN][1000 genomes]
rs10843824	0.86[ASN][1000 genomes]
rs10843827	0.85[ASN][1000 genomes]
rs10843828	0.85[ASN][1000 genomes]
rs10843829	0.83[ASN][1000 genomes]
rs10843831	0.84[ASN][1000 genomes]
rs10843832	0.85[ASN][1000 genomes]
rs10843834	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051005	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051008	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051010	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11051027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051045	0.86[ASN][1000 genomes]
rs11051047	0.85[ASN][1000 genomes]
rs11051048	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051049	0.85[ASN][1000 genomes]
rs11051050	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11051061	0.84[ASN][1000 genomes]
rs11051063	0.81[ASN][1000 genomes]
rs11835180	0.85[ASN][1000 genomes]
rs12146709	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12368923	0.86[ASN][1000 genomes]
rs12369125	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12370947	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12579616	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12809335	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12825440	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12826615	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12830910	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241828	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278558	0.89[EUR][1000 genomes]
rs2289302	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35133495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35336533	0.86[ASN][1000 genomes]
rs36074842	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4335626	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59177896	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61923728	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487934	0.86[ASN][1000 genomes]
rs6487936	0.86[ASN][1000 genomes]
rs7299800	0.86[ASN][1000 genomes]
rs7955804	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7958274	0.83[ASN][1000 genomes]
rs7958276	0.85[ASN][1000 genomes]
rs7966063	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979718	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7980510	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6487928	IPO8	Cis_1M	lymphoblastoid	RTeQTL
rs6487928	IPO8	cis	multi-tissue	Pritchard
rs6487928	IPO8	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30767000-30844200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:30780800-30847000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:30783800-30829000	Weak transcription	Small Intestine	intestine
4	chr12:30784800-30836600	Weak transcription	Fetal Heart	heart
5	chr12:30785000-30847800	Weak transcription	Gastric	stomach
6	chr12:30785200-30846400	Weak transcription	Spleen	Spleen
7	chr12:30785400-30847200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:30807800-30835200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr12:30808000-30837800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:30808400-30829800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:30808600-30830400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr12:30808600-30839200	Strong transcription	Liver	Liver
13	chr12:30808800-30835000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr12:30808800-30838000	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:30809200-30828800	Weak transcription	Pancreas	Pancrea
16	chr12:30810000-30838200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:30810800-30843200	Strong transcription	Dnd41	blood
18	chr12:30810800-30843800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:30811000-30844200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:30811200-30830200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr12:30812200-30832200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:30812200-30837400	Strong transcription	Primary B cells from peripheral blood	blood
23	chr12:30812600-30830200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:30812600-30844200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:30813000-30839400	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr12:30813200-30831600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:30813200-30844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:30813600-30831600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr12:30813600-30844200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:30815400-30845800	Weak transcription	Fetal Brain Male	brain
31	chr12:30816000-30829600	Weak transcription	HMEC	breast
32	chr12:30816200-30831600	Weak transcription	Hela-S3	cervix
33	chr12:30816200-30844000	Weak transcription	NHEK	skin
34	chr12:30816400-30844200	Weak transcription	NHLF	lung
35	chr12:30818000-30831800	Strong transcription	Primary B cells from cord blood	blood
36	chr12:30818600-30834800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:30820000-30828400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:30820600-30831000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:30820800-30836600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:30821000-30832400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:30821200-30828400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr12:30821400-30828400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr12:30821400-30834200	Weak transcription	Stomach Mucosa	stomach
44	chr12:30821600-30834800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:30821600-30837600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr12:30821600-30844200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr12:30821800-30829800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:30821800-30835400	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:30821800-30847200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:30821800-30847400	Weak transcription	Lung	lung

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