Variant report

Variant	rs12309028
Chromosome Location	chr12:49650541-49650542
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49644570..49652021-chr12:49657020..49661422,19	MCF-7	breast:
2	chr12:49650187..49651946-chr12:49687678..49689574,2	MCF-7	breast:
3	chr12:49523243..49526269-chr12:49642508..49650672,7	K562	blood:

Variant related genes	Relation type
ENSG00000123416	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000258101	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10047512	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10047588	1.00[AMR][1000 genomes]
rs1109811	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168925	1.00[AMR][1000 genomes]
rs11168927	1.00[AMR][1000 genomes]
rs11168928	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[AMR][1000 genomes]
rs11168931	0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs11168938	1.00[ASW][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168939	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168940	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168942	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11168955	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs11168956	0.82[AFR][1000 genomes]
rs11168957	0.82[AFR][1000 genomes]
rs11168958	0.82[AFR][1000 genomes]
rs12296231	1.00[ASW][hapmap];0.93[LWK][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12296536	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12297433	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12300386	1.00[AMR][1000 genomes]
rs12300998	1.00[AMR][1000 genomes]
rs12303188	0.87[YRI][hapmap]
rs12304259	1.00[ASW][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes]
rs12304483	1.00[AMR][1000 genomes]
rs12304746	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs12308571	0.82[AFR][1000 genomes]
rs12308782	0.81[AFR][1000 genomes]
rs12314967	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12318666	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12322876	1.00[AMR][1000 genomes]
rs28758893	1.00[AMR][1000 genomes]
rs9804936	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12309028	NOTUM	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49629200-49653400	Weak transcription	Fetal Kidney	kidney
2	chr12:49629400-49651000	Weak transcription	Fetal Brain Female	brain
3	chr12:49629400-49657800	Weak transcription	Fetal Stomach	stomach
4	chr12:49639600-49654000	Weak transcription	NHLF	lung
5	chr12:49639800-49653200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:49639800-49653200	Weak transcription	NHDF-Ad	bronchial
7	chr12:49639800-49653200	Weak transcription	Osteobl	bone
8	chr12:49639800-49653400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:49640200-49651000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr12:49640200-49653000	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:49645600-49654600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:49647200-49653200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:49647200-49653200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:49647200-49653200	Weak transcription	NHEK	skin
15	chr12:49647400-49653400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:49647400-49654600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:49648600-49651000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:49648600-49651400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:49649000-49653400	Weak transcription	A549	lung
20	chr12:49649800-49650600	Flanking Active TSS	HepG2	liver
21	chr12:49650000-49650600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:49650000-49657200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:49650000-49658000	Weak transcription	Right Atrium	heart
24	chr12:49650200-49651200	Enhancers	Ovary	ovary
25	chr12:49650200-49653600	Weak transcription	Hela-S3	cervix
26	chr12:49650200-49654400	Weak transcription	Placenta	Placenta
27	chr12:49650400-49652200	Enhancers	K562	blood

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