Variant report

Variant	rs12050076
Chromosome Location	chr14:70467658-70467659
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:70464835..70467780-chr14:70480239..70482134,2	MCF-7	breast:
2	chr14:70464914..70467730-chr14:70484220..70485964,2	MCF-7	breast:
3	chr14:70466020..70467833-chr14:70469835..70471870,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10134291	0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs10134965	0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs11158827	0.85[CHD][hapmap]
rs12050089	0.82[ASN][1000 genomes]
rs12101270	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12433177	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12885068	0.89[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12885683	0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs12887943	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12889195	0.82[ASN][1000 genomes]
rs12890357	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1459704	0.82[ASN][1000 genomes]
rs1471243	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs17107547	0.84[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17107592	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17107610	0.85[CHD][hapmap]
rs227405	0.82[CHB][hapmap]
rs227412	0.83[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs227416	0.83[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs227417	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs227419	0.82[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs227420	0.91[ASN][1000 genomes]
rs227422	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs227423	0.90[ASN][1000 genomes]
rs227424	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs227425	0.80[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs227426	0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs227427	0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs227437	0.84[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs227438	0.89[ASN][1000 genomes]
rs227439	0.89[ASN][1000 genomes]
rs227444	0.81[JPT][hapmap]
rs34311408	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3825739	0.89[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56031625	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56242824	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57609901	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60011612	0.81[AMR][1000 genomes]
rs61305	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs67294558	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7141378	0.81[ASN][1000 genomes]
rs7151788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7157226	0.81[ASN][1000 genomes]
rs7160726	0.81[ASN][1000 genomes]
rs8012912	0.85[CHD][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv832824	chr14:70320639-70511401	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12050076	SMOC1	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70439800-70477200	Weak transcription	Spleen	Spleen
2	chr14:70450600-70477200	Weak transcription	Fetal Brain Female	brain
3	chr14:70457800-70484800	Weak transcription	Brain Substantia Nigra	brain
4	chr14:70458600-70480800	Weak transcription	Brain Germinal Matrix	brain
5	chr14:70459000-70484800	Weak transcription	Gastric	stomach
6	chr14:70460000-70473800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr14:70460200-70468000	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr14:70460400-70472200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr14:70462000-70468600	Enhancers	HMEC	breast
10	chr14:70462200-70475600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr14:70462600-70467800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr14:70462600-70467800	Enhancers	NHEK	skin
13	chr14:70462600-70468000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr14:70462600-70468400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr14:70463000-70468000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr14:70463800-70469400	Enhancers	Pancreas	Pancrea
17	chr14:70464200-70468000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr14:70465000-70473600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:70465200-70477000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr14:70465400-70468200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr14:70465400-70468200	Enhancers	GM12878-XiMat	blood
22	chr14:70466000-70475600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr14:70466200-70471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr14:70466200-70484800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr14:70466600-70474400	Weak transcription	Fetal Stomach	stomach
26	chr14:70466800-70468400	Enhancers	A549	lung
27	chr14:70466800-70469800	Enhancers	Liver	Liver
28	chr14:70466800-70472400	Genic enhancers	Hela-S3	cervix
29	chr14:70467000-70468000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr14:70467000-70469200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr14:70467200-70469000	Enhancers	HepG2	liver
32	chr14:70467400-70469800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr14:70467600-70467800	Flanking Active TSS	Osteobl	bone
34	chr14:70467600-70468000	Enhancers	Primary B cells from peripheral blood	blood
35	chr14:70467600-70476000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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