Variant report

Variant	rs2304630
Chromosome Location	chr12:30881809-30881810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10444423	0.90[JPT][hapmap]
rs10743729	0.90[JPT][hapmap]
rs10743733	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10743734	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10771754	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10771764	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10771765	0.92[ASN][1000 genomes]
rs10771766	0.92[ASN][1000 genomes]
rs10771767	0.92[ASN][1000 genomes]
rs10771768	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10771769	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10843804	0.90[JPT][hapmap]
rs10843814	0.90[JPT][hapmap]
rs10843816	0.90[JPT][hapmap]
rs10843817	0.89[JPT][hapmap]
rs10843822	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10843824	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs10843833	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10843835	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11051005	0.90[JPT][hapmap]
rs11051013	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11051050	0.89[JPT][hapmap]
rs11051052	0.80[ASW][hapmap];0.92[CEU][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11051053	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11051061	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12146709	0.90[JPT][hapmap]
rs12303852	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12305697	0.92[ASN][1000 genomes]
rs12370429	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370947	0.90[JPT][hapmap]
rs12809335	0.84[JPT][hapmap]
rs12830910	0.90[JPT][hapmap]
rs13656	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1371049	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1371053	0.92[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1866416	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2099661	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2241828	0.90[JPT][hapmap]
rs2289301	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2289302	0.90[JPT][hapmap]
rs2352210	0.86[EUR][1000 genomes]
rs2352217	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs33132	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35925509	0.90[ASN][1000 genomes]
rs3782685	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4082413	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4143103	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4930935	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4930936	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4931356	0.85[EUR][1000 genomes]
rs6487932	0.96[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6487933	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6487938	0.89[ASN][1000 genomes]
rs6487939	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7136079	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs718368	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7298007	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7298180	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7304221	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7304879	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7304976	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311651	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs794152	0.85[CEU][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs7952744	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7957141	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7957226	0.92[ASN][1000 genomes]
rs7963494	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7968587	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7971762	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7971870	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7980510	0.90[JPT][hapmap]
rs9300199	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.91[EUR][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
rs2304630	IPO8	cis	multi-tissue	Pritchard
rs2304630	IPO8	cis	lymphoblastoid	seeQTL
rs2304630	IPO8	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30858000-30891800	Weak transcription	Fetal Heart	heart
2	chr12:30859200-30892200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:30859400-30883400	Weak transcription	Colonic Mucosa	Colon
4	chr12:30861400-30885000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:30861400-30906200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:30861400-30906600	Weak transcription	Small Intestine	intestine
7	chr12:30861800-30884600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:30861800-30894600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr12:30861800-30895200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr12:30862200-30895000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:30862400-30895600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:30863400-30882800	Weak transcription	Brain Substantia Nigra	brain
13	chr12:30863400-30885200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:30863400-30891000	Weak transcription	GM12878-XiMat	blood
15	chr12:30863400-30906400	Weak transcription	Spleen	Spleen
16	chr12:30863400-30906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:30864600-30905200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr12:30867400-30884400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:30869600-30886000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:30869800-30889000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:30871400-30900800	Weak transcription	K562	blood
22	chr12:30872200-30886000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:30872200-30903800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr12:30872400-30903000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:30873200-30882400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:30873600-30883800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:30874000-30884600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:30874600-30899000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr12:30875000-30883400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:30876000-30906600	Weak transcription	Fetal Intestine Small	intestine
31	chr12:30876200-30894800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr12:30878000-30899200	Weak transcription	Fetal Brain Male	brain
33	chr12:30878000-30904400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:30878000-30904400	Weak transcription	Pancreas	Pancrea
35	chr12:30878200-30906200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:30878800-30906600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr12:30879000-30884800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:30879400-30883000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:30879600-30899400	Weak transcription	NHDF-Ad	bronchial
40	chr12:30879800-30882600	Strong transcription	HMEC	breast
41	chr12:30879800-30883200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr12:30879800-30895000	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:30879800-30905800	Weak transcription	NHLF	lung
44	chr12:30880000-30883200	Strong transcription	Fetal Brain Female	brain
45	chr12:30880000-30883400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:30880000-30884600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:30880000-30893800	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr12:30880200-30882200	Strong transcription	Adipose Nuclei	Adipose
49	chr12:30880400-30882400	Strong transcription	Fetal Kidney	kidney
50	chr12:30880400-30884800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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