Variant report

Variant	rs10843820
Chromosome Location	chr12:30867794-30867795
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10444423	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10734793	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743729	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10771756	0.83[ASN][1000 genomes]
rs10771757	0.85[ASN][1000 genomes]
rs10771760	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771761	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771762	0.93[ASN][1000 genomes]
rs10771768	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs10843804	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10843813	0.81[ASN][1000 genomes]
rs10843814	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10843815	0.93[ASN][1000 genomes]
rs10843816	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10843817	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10843818	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843819	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843821	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843822	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843823	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843827	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843828	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843829	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10843831	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843832	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843833	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs10843834	0.91[ASN][1000 genomes]
rs10843835	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11051005	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11051010	0.80[ASN][1000 genomes]
rs11051027	0.85[ASN][1000 genomes]
rs11051045	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11051047	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051048	0.93[ASN][1000 genomes]
rs11051049	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051050	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs11051053	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs11051061	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[ASN][1000 genomes]
rs11051063	0.87[ASN][1000 genomes]
rs11835180	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12146709	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12303852	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs12320609	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12368923	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369125	0.80[ASN][1000 genomes]
rs12370947	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12809335	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12809355	0.85[ASN][1000 genomes]
rs12825440	0.82[ASN][1000 genomes]
rs12826615	0.82[ASN][1000 genomes]
rs12830910	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2241828	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2289302	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2304630	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs35133495	0.94[ASN][1000 genomes]
rs35336533	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4082413	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4335626	0.82[ASN][1000 genomes]
rs59177896	0.82[ASN][1000 genomes]
rs61923728	0.94[ASN][1000 genomes]
rs6487928	0.86[ASN][1000 genomes]
rs6487933	0.86[CHB][hapmap]
rs6487934	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487939	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7299800	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304221	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7952744	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7955804	0.82[ASN][1000 genomes]
rs7957141	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7958274	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7958276	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7966063	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7971762	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs7971870	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs7979718	0.82[ASN][1000 genomes]
rs7980510	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[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
rs10843820	IPO8	cis	cerebellum	SCAN
rs10843820	C12orf35	cis	parietal	SCAN
rs10843820	FLJ13224	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30849200-30881600	Weak transcription	Right Ventricle	heart
2	chr12:30849600-30881200	Weak transcription	Psoas Muscle	Psoas
3	chr12:30849600-30881600	Weak transcription	Aorta	Aorta
4	chr12:30857400-30881800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:30858000-30891800	Weak transcription	Fetal Heart	heart
6	chr12:30858800-30868600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:30859000-30869400	Weak transcription	K562	blood
8	chr12:30859200-30892200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:30859400-30883400	Weak transcription	Colonic Mucosa	Colon
10	chr12:30859800-30877000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:30860200-30871200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:30860400-30881600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:30861000-30879000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:30861200-30871400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:30861200-30875000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:30861400-30869800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:30861400-30872600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:30861400-30881600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:30861400-30885000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:30861400-30906200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr12:30861400-30906600	Weak transcription	Small Intestine	intestine
22	chr12:30861800-30869800	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr12:30861800-30870000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:30861800-30872000	Strong transcription	HSMM	muscle
25	chr12:30861800-30872600	Strong transcription	Fetal Brain Female	brain
26	chr12:30861800-30872800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr12:30861800-30877800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:30861800-30879000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr12:30861800-30884600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:30861800-30894600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:30861800-30895200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:30862000-30869600	Strong transcription	Fetal Muscle Leg	muscle
33	chr12:30862000-30871800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:30862000-30872200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:30862000-30872600	Strong transcription	Liver	Liver
36	chr12:30862000-30877800	Strong transcription	HMEC	breast
37	chr12:30862000-30878800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:30862000-30879000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr12:30862200-30872200	Strong transcription	Brain Anterior Caudate	brain
40	chr12:30862200-30879000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:30862200-30895000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:30862400-30871000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:30862400-30871200	Strong transcription	Adipose Nuclei	Adipose
44	chr12:30862400-30872000	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr12:30862400-30872400	Strong transcription	Primary T cells from cord blood	blood
46	chr12:30862400-30876600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:30862400-30895600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:30862600-30870400	Strong transcription	A549	lung
49	chr12:30862600-30872400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:30862600-30872400	Strong transcription	Monocytes-CD14+_RO01746	blood

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