Variant report

Variant	rs11608811
Chromosome Location	chr12:123529056-123529057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123527949..123530263-chr12:124116742..124119080,2	MCF-7	breast:
2	chr12:123527736..123529546-chr12:123540101..123542162,2	K562	blood:
3	chr12:123527304..123529634-chr12:123630952..123633326,2	MCF-7	breast:
4	chr12:123527596..123531182-chr12:123539339..123542162,4	K562	blood:
5	chr12:123519670..123521878-chr12:123527130..123529862,2	MCF-7	breast:
6	chr12:123526656..123529148-chr12:123634939..123636869,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111361	Chromatin interaction
ENSG00000111358	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1051434	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs10773921	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10848428	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11060853	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs11613937	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12425009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12425850	1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1615350	0.83[CHB][hapmap];0.82[TSI][hapmap]
rs1727293	0.90[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs1727295	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap]
rs1727302	0.83[CHB][hapmap];0.82[TSI][hapmap]
rs1727307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790104	1.00[YRI][hapmap]
rs1790106	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1790122	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1879379	0.90[ASW][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs1984658	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28755851	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3741530	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3759115	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3897102	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4148862	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4148863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4148866	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs4275659	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55742290	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs585522	0.80[GIH][hapmap]
rs61955196	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61955214	0.88[ASN][1000 genomes]
rs7135296	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7139321	1.00[YRI][hapmap]
rs7296418	0.91[CEU][hapmap];0.95[CHB][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7305511	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7957096	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883562	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs884956	0.90[ASW][hapmap];0.95[CHB][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs940904	0.80[GIH][hapmap]
rs949143	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11608811	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs11608811	CDK2AP1	cis	cerebellum	SCAN
rs11608811	PITPNM2	cis	cerebellum	SCAN
rs11608811	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs11608811	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs11608811	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs11608811	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs11608811	C12orf65	cis	cerebellum	SCAN
rs11608811	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs11608811	TMEM120B	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123504400-123540200	Weak transcription	Hela-S3	cervix
2	chr12:123509800-123530400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:123518200-123535600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:123518400-123533600	Weak transcription	Aorta	Aorta
5	chr12:123518800-123540600	Weak transcription	HepG2	liver
6	chr12:123519000-123540400	Weak transcription	Gastric	stomach
7	chr12:123519000-123543400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:123525400-123529400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:123525400-123530000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:123526000-123529800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
11	chr12:123526000-123531000	Enhancers	Placenta	Placenta
12	chr12:123526000-123531400	Enhancers	Colon Smooth Muscle	Colon
13	chr12:123526400-123529200	Enhancers	NHLF	lung
14	chr12:123526400-123530400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr12:123526400-123530800	Enhancers	Fetal Muscle Leg	muscle
16	chr12:123526400-123531000	Enhancers	Brain Cingulate Gyrus	brain
17	chr12:123526400-123531000	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr12:123526400-123531600	Enhancers	Rectal Smooth Muscle	rectum
19	chr12:123526600-123530800	Enhancers	Left Ventricle	heart
20	chr12:123526600-123531200	Enhancers	Right Atrium	heart
21	chr12:123526800-123530600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr12:123526800-123531200	Enhancers	Fetal Heart	heart
23	chr12:123527200-123529200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:123527200-123529200	Enhancers	Primary hematopoietic stem cells	blood
25	chr12:123527200-123529200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:123527200-123529800	Enhancers	Liver	Liver
27	chr12:123527400-123529200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr12:123527400-123529400	Enhancers	Brain Hippocampus Middle	brain
29	chr12:123527400-123529400	Enhancers	Small Intestine	intestine
30	chr12:123527400-123530800	Enhancers	Colonic Mucosa	Colon
31	chr12:123527400-123531400	Enhancers	Fetal Stomach	stomach
32	chr12:123527600-123529200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr12:123527600-123529600	Enhancers	Primary T cells fromperipheralblood	blood
34	chr12:123527600-123529800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr12:123527600-123530200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:123527800-123529200	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr12:123527800-123529200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:123527800-123529200	Enhancers	Primary B cells from cord blood	blood
39	chr12:123527800-123529200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:123527800-123529200	Enhancers	NHDF-Ad	bronchial
41	chr12:123527800-123529600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:123527800-123529600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr12:123527800-123530200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr12:123528000-123529200	Enhancers	Adipose Nuclei	Adipose
45	chr12:123528000-123529200	Enhancers	Spleen	Spleen
46	chr12:123528000-123529400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr12:123528000-123529600	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr12:123528000-123529800	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr12:123528000-123530200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr12:123528200-123529200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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