Variant report

Variant	rs12425009
Chromosome Location	chr12:123502044-123502045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123495256..123498165-chr12:123500426..123502065,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265526	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1051434	0.96[CEU][hapmap];0.82[CHB][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];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10848428	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11060853	0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11608811	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]
rs11613937	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12425850	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.84[LWK][hapmap];1.00[MEX][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];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1790094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1790106	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1790121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1790122	0.82[EUR][1000 genomes]
rs1984658	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28755851	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741530	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3759115	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3897102	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs4148862	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4148863	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4148866	0.84[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4275659	0.90[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55742290	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61955196	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61955214	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7135296	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7296418	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305511	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957096	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs883562	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs884956	0.90[ASW][hapmap];0.95[CHB][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs949143	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12425009	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs12425009	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs12425009	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs12425009	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs12425009	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs12425009	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 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	chr12:123469400-123509400	Weak transcription	NHDF-Ad	bronchial
4	chr12:123469400-123509600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr12:123470200-123512800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr12:123470400-123526600	Weak transcription	Fetal Lung	lung
7	chr12:123489200-123512400	Weak transcription	Aorta	Aorta
8	chr12:123490000-123515800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:123490200-123503600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:123490200-123511000	Weak transcription	Pancreas	Pancrea
11	chr12:123490200-123528200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:123490400-123503200	Weak transcription	NHEK	skin
13	chr12:123490400-123503800	Weak transcription	A549	lung
14	chr12:123491200-123503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:123491600-123526400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:123491800-123503400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:123492000-123518600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:123492200-123503600	Weak transcription	Osteobl	bone
19	chr12:123492600-123515800	Weak transcription	Fetal Brain Male	brain
20	chr12:123492800-123504200	Weak transcription	K562	blood
21	chr12:123492800-123509400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:123493600-123517600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr12:123493800-123503000	Weak transcription	HMEC	breast
24	chr12:123494000-123509000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:123494400-123503800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:123494400-123504200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:123494400-123511800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:123494400-123517800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:123494400-123518000	Weak transcription	Brain Substantia Nigra	brain
30	chr12:123494600-123503000	Weak transcription	Fetal Intestine Large	intestine
31	chr12:123494600-123503400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:123494600-123503600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:123494600-123503800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:123494600-123504000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:123494600-123510600	Weak transcription	Brain Anterior Caudate	brain
36	chr12:123494600-123510800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:123494800-123517000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:123495000-123514000	Weak transcription	Brain Angular Gyrus	brain
39	chr12:123495200-123512800	Weak transcription	Brain Germinal Matrix	brain
40	chr12:123495600-123509800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:123495800-123503800	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:123496000-123511200	Weak transcription	Esophagus	oesophagus
43	chr12:123496000-123526400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:123496200-123504000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr12:123496600-123504000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:123496600-123517600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:123497200-123509800	Weak transcription	Fetal Brain Female	brain
48	chr12:123497200-123517200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:123497200-123517600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr12:123497400-123528600	Weak transcription	Ovary	ovary

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