Variant report

Variant	rs7952760
Chromosome Location	chr12:123543647-123543648
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	chr12:123444883..123447117-chr12:123541287..123543838,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11060932	0.94[YRI][hapmap]
rs11060999	1.00[ASW][hapmap];0.83[LWK][hapmap];0.94[YRI][hapmap]
rs11061578	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12229712	0.80[AFR][1000 genomes]
rs12311043	1.00[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.94[YRI][hapmap]
rs34010146	0.81[AFR][1000 genomes]
rs4427600	0.81[ASW][hapmap];0.81[LWK][hapmap];1.00[MKK][hapmap]
rs55796417	0.97[AFR][1000 genomes]
rs55813219	0.86[AFR][1000 genomes]
rs55830208	0.97[AFR][1000 genomes]
rs55951195	0.86[AFR][1000 genomes]
rs55992397	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56020503	0.97[AFR][1000 genomes]
rs56140750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56288804	0.83[AFR][1000 genomes]
rs56725866	0.97[AFR][1000 genomes]
rs57106451	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57178349	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57641050	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57719471	1.00[AMR][1000 genomes]
rs57764857	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57794792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57863319	0.81[AFR][1000 genomes]
rs58025094	0.81[AFR][1000 genomes]
rs58339539	0.85[AMR][1000 genomes]
rs58462666	0.86[AFR][1000 genomes]
rs59211448	0.81[AFR][1000 genomes]
rs59379557	0.83[AFR][1000 genomes]
rs59615440	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59881907	1.00[AMR][1000 genomes]
rs60341839	0.97[AFR][1000 genomes]
rs60341983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60358140	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60546720	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60761837	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60809882	0.97[AFR][1000 genomes]
rs60888713	0.86[AFR][1000 genomes]
rs60987910	0.83[AFR][1000 genomes]
rs61061591	0.86[AFR][1000 genomes]
rs61377358	0.97[AFR][1000 genomes]
rs61516893	0.97[AFR][1000 genomes]
rs61546241	0.83[AFR][1000 genomes]
rs61592192	0.83[AFR][1000 genomes]
rs61677786	0.83[AFR][1000 genomes]
rs7302112	1.00[AMR][1000 genomes]
rs73408899	0.81[AFR][1000 genomes]
rs73411006	0.86[AFR][1000 genomes]
rs73411009	0.86[AFR][1000 genomes]
rs73411011	0.86[AFR][1000 genomes]
rs73411015	0.86[AFR][1000 genomes]
rs73411018	0.86[AFR][1000 genomes]
rs73411027	0.83[AFR][1000 genomes]
rs73411033	0.83[AFR][1000 genomes]
rs73411041	0.83[AFR][1000 genomes]
rs73411043	0.83[AFR][1000 genomes]
rs73411057	0.97[AFR][1000 genomes]
rs73411058	0.97[AFR][1000 genomes]
rs73411063	0.97[AFR][1000 genomes]
rs73411076	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411084	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411088	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411090	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411093	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73411098	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73413226	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413228	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413230	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413236	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413241	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413246	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413263	1.00[AMR][1000 genomes]
rs73413265	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73413270	1.00[AMR][1000 genomes]
rs73417317	0.85[AMR][1000 genomes]
rs73417324	0.85[AMR][1000 genomes]
rs752164	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs7957096	1.00[YRI][hapmap]
rs7964036	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	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
9	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7952760	ARL6IP4	cis	multi-tissue	Pritchard
rs7952760	OGFOD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123528600-123545800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:123529400-123544600	Weak transcription	Small Intestine	intestine
3	chr12:123529600-123546200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr12:123529800-123548200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:123530800-123544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr12:123532400-123546600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:123534800-123547200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:123536000-123544200	Weak transcription	Liver	Liver
9	chr12:123537800-123551200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:123538800-123543800	Genic enhancers	Fetal Thymus	thymus
11	chr12:123538800-123544200	Strong transcription	Primary T cells from cord blood	blood
12	chr12:123539400-123546600	Weak transcription	HSMMtube	muscle
13	chr12:123539600-123546000	Genic enhancers	Thymus	Thymus
14	chr12:123539600-123552600	Enhancers	Right Ventricle	heart
15	chr12:123539800-123549600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr12:123540000-123547200	Weak transcription	NH-A	brain
17	chr12:123540000-123547400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:123540200-123543800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:123540400-123544000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:123540600-123544000	Weak transcription	Fetal Brain Female	brain
21	chr12:123540600-123547400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:123540800-123544000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:123541000-123543800	Weak transcription	Esophagus	oesophagus
24	chr12:123541000-123545200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:123541000-123546600	Weak transcription	HepG2	liver
26	chr12:123541200-123543800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:123541200-123545800	Weak transcription	HSMM	muscle
28	chr12:123541200-123546200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr12:123541200-123547000	Weak transcription	A549	lung
30	chr12:123541200-123548000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:123541400-123544000	Weak transcription	Psoas Muscle	Psoas
32	chr12:123541600-123545400	Weak transcription	Pancreas	Pancrea
33	chr12:123541600-123546600	Weak transcription	Hela-S3	cervix
34	chr12:123541800-123551200	Enhancers	Fetal Muscle Leg	muscle
35	chr12:123542200-123547000	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr12:123542200-123547400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:123542200-123551200	Enhancers	Fetal Muscle Trunk	muscle
38	chr12:123542600-123546800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:123542600-123550400	Enhancers	NHDF-Ad	bronchial
40	chr12:123542600-123550600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:123542600-123550800	Enhancers	Placenta	Placenta
42	chr12:123542800-123543800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:123542800-123545200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:123542800-123546000	Enhancers	Brain Angular Gyrus	brain
45	chr12:123542800-123547000	Enhancers	Fetal Heart	heart
46	chr12:123542800-123563800	Enhancers	Left Ventricle	heart
47	chr12:123543000-123546600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr12:123543000-123547600	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr12:123543000-123549600	Enhancers	NHLF	lung
50	chr12:123543000-123551400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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