Variant report

Variant	rs11060999
Chromosome Location	chr12:123441675-123441676
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123354937..123357622-chr12:123439392..123442120,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139722	Chromatin interaction

Extended variants
information (count: 121 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10219462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1026395	1.00[JPT][hapmap]
rs1037593	1.00[JPT][hapmap]
rs10431343	1.00[CHB][hapmap]
rs10773599	1.00[JPT][hapmap]
rs10846468	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10846469	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10846471	0.87[GIH][hapmap];1.00[JPT][hapmap]
rs10846473	0.87[ASN][1000 genomes]
rs10847742	1.00[JPT][hapmap]
rs10847749	1.00[JPT][hapmap]
rs10847751	1.00[JPT][hapmap]
rs10847775	1.00[JPT][hapmap]
rs10847910	1.00[JPT][hapmap]
rs10848148	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848363	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848365	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10848429	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs11057172	0.87[ASN][1000 genomes]
rs11060152	1.00[JPT][hapmap]
rs11060888	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060932	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11060997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061166	0.87[ASN][1000 genomes]
rs11061601	0.87[ASN][1000 genomes]
rs11061611	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11061616	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12229119	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298355	0.87[ASN][1000 genomes]
rs12306711	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12311043	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311134	0.87[ASN][1000 genomes]
rs12318594	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12366787	0.87[ASN][1000 genomes]
rs1260121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1671684	1.00[JPT][hapmap]
rs1671687	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1696355	1.00[CHB][hapmap]
rs1798563	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1975761	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2061099	1.00[JPT][hapmap]
rs2343107	1.00[JPT][hapmap]
rs2649895	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2649900	1.00[CHB][hapmap]
rs2649903	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2656812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34010146	0.92[AFR][1000 genomes]
rs3844369	1.00[JPT][hapmap]
rs4307760	1.00[JPT][hapmap]
rs4427600	0.83[ASW][hapmap]
rs4759353	1.00[JPT][hapmap]
rs4759354	1.00[JPT][hapmap]
rs4759384	1.00[JPT][hapmap]
rs4759438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55813219	0.86[AFR][1000 genomes]
rs55951195	0.86[AFR][1000 genomes]
rs56150478	0.85[AFR][1000 genomes]
rs56288804	0.89[AFR][1000 genomes]
rs57110420	0.82[AFR][1000 genomes]
rs57310784	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57863319	0.86[AFR][1000 genomes]
rs58025094	0.92[AFR][1000 genomes]
rs58462666	0.86[AFR][1000 genomes]
rs59002329	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59081274	0.93[AFR][1000 genomes]
rs59211448	0.86[AFR][1000 genomes]
rs59379557	0.89[AFR][1000 genomes]
rs59526938	0.92[AFR][1000 genomes]
rs60888713	0.86[AFR][1000 genomes]
rs60987910	0.89[AFR][1000 genomes]
rs61061591	0.86[AFR][1000 genomes]
rs61546241	0.89[AFR][1000 genomes]
rs61592192	0.89[AFR][1000 genomes]
rs61677786	0.89[AFR][1000 genomes]
rs7138257	1.00[JPT][hapmap]
rs7295258	0.81[AFR][1000 genomes]
rs7298176	1.00[JPT][hapmap]
rs7306948	1.00[JPT][hapmap]
rs73408835	0.92[AFR][1000 genomes]
rs73408859	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408862	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408863	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408890	0.94[AFR][1000 genomes]
rs73408892	0.94[AFR][1000 genomes]
rs73408893	0.93[AFR][1000 genomes]
rs73408894	0.94[AFR][1000 genomes]
rs73408899	0.92[AFR][1000 genomes]
rs73411006	0.86[AFR][1000 genomes]
rs73411009	0.86[AFR][1000 genomes]
rs73411011	0.86[AFR][1000 genomes]
rs73411014	0.81[AFR][1000 genomes]
rs73411015	0.86[AFR][1000 genomes]
rs73411018	0.86[AFR][1000 genomes]
rs73411027	0.89[AFR][1000 genomes]
rs73411033	0.89[AFR][1000 genomes]
rs73411041	0.89[AFR][1000 genomes]
rs73411043	0.89[AFR][1000 genomes]
rs7485652	1.00[JPT][hapmap]
rs752164	1.00[ASW][hapmap];0.83[LWK][hapmap];0.94[YRI][hapmap]
rs7952760	1.00[ASW][hapmap];0.83[LWK][hapmap];0.94[YRI][hapmap]
rs7957096	0.94[YRI][hapmap]
rs7957643	1.00[JPT][hapmap]
rs7958155	1.00[JPT][hapmap]
rs7964036	1.00[ASW][hapmap];0.83[LWK][hapmap];0.94[YRI][hapmap]
rs839354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs897388	1.00[JPT][hapmap]
rs967281	1.00[JPT][hapmap]
rs9795629	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv560491	chr12:123425575-123444422	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv899577	chr12:123435248-123484474	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11060999	OGFOD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123403000-123444200	Weak transcription	Aorta	Aorta
2	chr12:123412800-123449200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123413400-123449600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:123413600-123450000	Weak transcription	Primary T cells from cord blood	blood
5	chr12:123417400-123441800	Weak transcription	Ovary	ovary
6	chr12:123417600-123446200	Weak transcription	Fetal Lung	lung
7	chr12:123429600-123444000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:123429800-123444000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:123430000-123441800	Weak transcription	Fetal Brain Male	brain
10	chr12:123432000-123444000	Weak transcription	Thymus	Thymus
11	chr12:123432200-123441800	Weak transcription	Right Ventricle	heart
12	chr12:123432200-123444200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr12:123432200-123446000	Weak transcription	Right Atrium	heart
14	chr12:123432200-123446000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:123432200-123446000	Weak transcription	K562	blood
16	chr12:123432200-123450000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:123432200-123450200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr12:123432400-123444200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:123432400-123444200	Weak transcription	Pancreas	Pancrea
20	chr12:123432400-123448200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:123432400-123449600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:123432400-123450000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:123432600-123444200	Weak transcription	Esophagus	oesophagus
24	chr12:123432600-123444200	Weak transcription	Spleen	Spleen
25	chr12:123432600-123444400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr12:123432600-123448200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:123432600-123450000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:123433000-123441800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:123433200-123441800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:123435000-123443000	Weak transcription	Brain Anterior Caudate	brain
31	chr12:123435200-123442800	Weak transcription	Brain Substantia Nigra	brain
32	chr12:123435200-123444200	Weak transcription	Gastric	stomach
33	chr12:123435400-123444000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:123436400-123441800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:123436400-123444000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:123436400-123444200	Weak transcription	NHLF	lung
37	chr12:123436400-123448000	Weak transcription	HepG2	liver
38	chr12:123436600-123444000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:123436600-123446000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr12:123436600-123446000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:123436600-123449400	Weak transcription	NHDF-Ad	bronchial
42	chr12:123436800-123441800	Weak transcription	HUVEC	blood vessel
43	chr12:123436800-123442800	Weak transcription	Fetal Intestine Large	intestine
44	chr12:123436800-123443800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:123436800-123444000	Weak transcription	HMEC	breast
46	chr12:123436800-123444400	Weak transcription	NHEK	skin
47	chr12:123436800-123446200	Weak transcription	A549	lung
48	chr12:123436800-123448600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:123437000-123446000	Weak transcription	Hela-S3	cervix
50	chr12:123437200-123445800	Weak transcription	Rectal Mucosa Donor 31	rectum

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