Variant report

Variant	rs883263
Chromosome Location	chr12:123485188-123485189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123474530..123476275-chr12:123483617..123485746,2	K562	blood:
2	chr12:123483916..123486728-chr12:123489972..123492834,2	K562	blood:
3	chr12:123467378..123471463-chr12:123484194..123486166,3	MCF-7	breast:
4	chr12:123479422..123482791-chr12:123483500..123486744,3	K562	blood:

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1051431	0.88[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap]
rs1106240	0.88[CEU][hapmap];0.85[GIH][hapmap];0.94[TSI][hapmap]
rs1106241	0.88[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs1260294	0.94[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs12811109	0.96[EUR][1000 genomes]
rs12820906	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12828755	0.96[EUR][1000 genomes]
rs1463877	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569068	0.88[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap]
rs1615350	0.81[GIH][hapmap];0.81[TSI][hapmap]
rs1617156	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs1716157	0.88[CEU][hapmap];0.97[TSI][hapmap]
rs1716164	0.88[CEU][hapmap];0.97[TSI][hapmap]
rs1716165	0.88[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap]
rs1716167	0.88[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs1716168	0.88[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs1716175	0.88[CEU][hapmap]
rs1716176	0.88[CEU][hapmap]
rs1716177	0.88[CEU][hapmap]
rs1727294	0.85[CEU][hapmap];0.81[ASN][1000 genomes]
rs1727296	0.88[CEU][hapmap]
rs1727302	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs1727306	0.88[CEU][hapmap]
rs1727309	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs1727313	0.88[CEU][hapmap];0.94[TSI][hapmap]
rs1727315	0.88[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap]
rs1790095	0.88[CEU][hapmap];0.97[TSI][hapmap]
rs1790098	0.88[CEU][hapmap];0.97[TSI][hapmap]
rs1790100	0.88[CEU][hapmap]
rs1790108	0.88[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs1790116	0.82[CEU][hapmap];0.85[GIH][hapmap];0.97[TSI][hapmap]
rs1790123	0.88[CEU][hapmap];0.94[TSI][hapmap]
rs2049114	0.88[CEU][hapmap]
rs2270789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2510885	0.81[ASN][1000 genomes]
rs2695482	0.88[CEU][hapmap]
rs2851447	0.81[CEU][hapmap]
rs4148856	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4460848	0.84[TSI][hapmap]
rs520088	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585522	1.00[ASW][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.85[LWK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs641760	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs655293	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7132277	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs71444568	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7296418	0.81[MEX][hapmap];0.83[YRI][hapmap]
rs7299943	0.92[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs883563	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs884548	0.88[CEU][hapmap]
rs937564	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs940904	0.93[ASW][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
8	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs883263	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs883263	MPHOSPH9	cis	Esophagus Muscularis	GTEx
rs883263	RP11-282O18.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123466800-123516000	Weak transcription	Small Intestine	intestine
2	chr12:123467600-123504000	Weak transcription	Hela-S3	cervix
3	chr12:123468000-123486200	Strong transcription	Fetal Brain Female	brain
4	chr12:123468800-123485200	Weak transcription	Aorta	Aorta
5	chr12:123469200-123498600	Strong transcription	Primary T cells from cord blood	blood
6	chr12:123469400-123491600	Weak transcription	HMEC	breast
7	chr12:123469400-123509400	Weak transcription	NHDF-Ad	bronchial
8	chr12:123469400-123509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:123469600-123493200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:123469800-123485800	Strong transcription	Placenta	Placenta
11	chr12:123469800-123486800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:123469800-123491400	Weak transcription	HSMMtube	muscle
13	chr12:123469800-123491600	Weak transcription	Osteobl	bone
14	chr12:123470000-123486200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:123470000-123486200	Weak transcription	HSMM	muscle
16	chr12:123470000-123486600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:123470200-123512800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:123470400-123526600	Weak transcription	Fetal Lung	lung
19	chr12:123470600-123486200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:123472000-123499000	Strong transcription	Thymus	Thymus
21	chr12:123472400-123491400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:123472600-123492800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr12:123472800-123494200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:123472800-123500400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:123473200-123489400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:123473200-123489400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:123473200-123491200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr12:123473400-123501000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:123473800-123492600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:123473800-123500800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:123475600-123491400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr12:123476400-123485200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:123478200-123485800	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr12:123478400-123486800	Strong transcription	Fetal Stomach	stomach
35	chr12:123479200-123485400	Weak transcription	Fetal Intestine Large	intestine
36	chr12:123479200-123485600	Strong transcription	Fetal Intestine Small	intestine
37	chr12:123479200-123486000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:123479400-123485800	Strong transcription	Ovary	ovary
39	chr12:123479800-123489400	Weak transcription	A549	lung
40	chr12:123480600-123485600	Strong transcription	Brain Germinal Matrix	brain
41	chr12:123480800-123485400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr12:123480800-123487600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr12:123481200-123485200	Weak transcription	Right Atrium	heart
44	chr12:123481200-123485400	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:123481200-123485600	Strong transcription	Colonic Mucosa	Colon
46	chr12:123481200-123486200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:123481200-123486400	Strong transcription	Right Ventricle	heart
48	chr12:123481400-123485800	Strong transcription	Lung	lung
49	chr12:123481400-123491800	Weak transcription	HepG2	liver
50	chr12:123481600-123485800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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