Variant report

Variant	rs28406193
Chromosome Location	chr12:123891865-123891866
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123889713..123892231-chr12:123892398..123893927,2	K562	blood:
2	chr12:123889075..123892344-chr12:123892398..123894933,4	K562	blood:
3	chr12:123886695..123888203-chr12:123890596..123893402,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1060105	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10772998	0.83[CEU][hapmap]
rs10773002	0.81[GIH][hapmap]
rs10846486	0.89[CEU][hapmap]
rs11057192	0.83[CEU][hapmap];0.97[TSI][hapmap]
rs11830103	0.92[CEU][hapmap]
rs12298826	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs12299125	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs12304248	0.89[CEU][hapmap]
rs12316131	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs12322888	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs12817892	0.91[CEU][hapmap]
rs1402275	0.93[GIH][hapmap]
rs1533703	0.81[CEU][hapmap]
rs1568427	0.85[GIH][hapmap]
rs1609520	0.85[GIH][hapmap]
rs1716160	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1716170	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1716171	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1727320	0.89[CEU][hapmap]
rs1727323	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1727324	0.89[CEU][hapmap]
rs1727325	0.89[CEU][hapmap]
rs1727331	0.85[GIH][hapmap]
rs1790131	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs1879380	0.89[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs1969354	0.84[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs1980252	0.84[CEU][hapmap]
rs2337934	0.84[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap]
rs2682434	0.89[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs28372579	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28376121	0.82[EUR][1000 genomes]
rs28410896	0.80[EUR][1000 genomes]
rs28413626	0.87[EUR][1000 genomes]
rs28458312	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes]
rs28472704	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28481863	0.87[EUR][1000 genomes]
rs28569885	0.83[CEU][hapmap];0.94[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs28576953	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28582096	0.91[EUR][1000 genomes]
rs28583837	0.92[EUR][1000 genomes]
rs28592876	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28625019	0.89[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs28636834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28675824	0.88[EUR][1000 genomes]
rs28676499	0.88[EUR][1000 genomes]
rs28683528	0.86[EUR][1000 genomes]
rs28706696	0.89[CEU][hapmap];0.94[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs28715490	0.89[EUR][1000 genomes]
rs28809230	0.89[EUR][1000 genomes]
rs28855757	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4372492	0.89[CEU][hapmap]
rs4759371	0.84[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs4759409	0.84[CEU][hapmap]
rs4759415	0.84[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap]
rs4930718	0.91[GIH][hapmap];0.88[TSI][hapmap]
rs4930719	0.88[EUR][1000 genomes]
rs6488868	0.88[ASW][hapmap]
rs6576	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7304782	0.85[GIH][hapmap]
rs7313483	0.83[CEU][hapmap]
rs7485502	0.84[EUR][1000 genomes]
rs7953929	0.89[CEU][hapmap];0.93[GIH][hapmap]
rs7980687	0.89[CEU][hapmap]
rs941305	0.89[CEU][hapmap]
rs941306	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv975550	chr12:123888322-123893712	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv975551	chr12:123888322-123897046	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
7	esv3390116	chr12:123889494-123892144	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3448883	chr12:123889563-123892089	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1398988	chr12:123891865-123891866	Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28406193	CDK2AP1	cis	lymphoblastoid	seeQTL
rs28406193	PITPNM2	cis	cerebellum	SCAN
rs28406193	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28406193	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28406193	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28406193	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28406193	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs28406193	ANAPC5	cis	parietal	SCAN
rs28406193	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28406193	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123875200-123894400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:123875600-123894200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:123875600-123895600	Strong transcription	Fetal Thymus	thymus
4	chr12:123875800-123894000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:123876400-123894800	Strong transcription	Fetal Intestine Small	intestine
6	chr12:123876600-123894800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:123877400-123895600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:123882000-123911600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:123883200-123895400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:123883800-123894200	Strong transcription	HUVEC	blood vessel
11	chr12:123883800-123895200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:123884200-123892800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:123884200-123895200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr12:123886000-123895200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:123886000-123895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:123886200-123892000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:123886200-123892000	Strong transcription	Primary T cells from cord blood	blood
18	chr12:123886200-123894200	Strong transcription	Fetal Intestine Large	intestine
19	chr12:123886200-123894800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:123886200-123895200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:123886200-123895200	Strong transcription	Fetal Muscle Leg	muscle
22	chr12:123886200-123895200	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:123886200-123895200	Strong transcription	Dnd41	blood
24	chr12:123886200-123895400	Strong transcription	Fetal Brain Female	brain
25	chr12:123886400-123892200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:123886400-123892200	Strong transcription	Brain Germinal Matrix	brain
27	chr12:123886400-123892400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:123886400-123893400	Strong transcription	Rectal Smooth Muscle	rectum
29	chr12:123886400-123894200	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr12:123886400-123894200	Strong transcription	Left Ventricle	heart
31	chr12:123886400-123894200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr12:123886400-123894400	Strong transcription	Osteobl	bone
33	chr12:123886400-123894800	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr12:123886400-123895000	Strong transcription	Adipose Nuclei	Adipose
35	chr12:123886400-123895000	Strong transcription	Liver	Liver
36	chr12:123886400-123895200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:123886400-123895200	Strong transcription	Spleen	Spleen
38	chr12:123886400-123895200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr12:123886400-123895200	Strong transcription	NHLF	lung
40	chr12:123886400-123895400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:123886400-123895400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:123886400-123895400	Strong transcription	Thymus	Thymus
43	chr12:123886600-123892000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:123886600-123892200	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr12:123886600-123892600	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr12:123886600-123892800	Strong transcription	Aorta	Aorta
47	chr12:123886600-123894000	Strong transcription	HSMMtube	muscle
48	chr12:123886600-123894200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr12:123886600-123894200	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr12:123886600-123894200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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