Variant report

Variant	rs12885683
Chromosome Location	chr14:70477942-70477943
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	chr14:70464484..70467038-chr14:70477152..70479604,2	MCF-7	breast:
2	chr14:70476343..70479164-chr14:70482815..70484444,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1005543	0.82[CHB][hapmap]
rs10134291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10134965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10136848	1.00[YRI][hapmap]
rs10138444	1.00[YRI][hapmap]
rs10139843	1.00[YRI][hapmap]
rs11158827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs12050076	0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs12050089	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12101270	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12433177	0.84[CHD][hapmap]
rs12878947	0.81[ASN][1000 genomes]
rs12885068	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12887943	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12889195	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12890357	0.90[ASN][1000 genomes]
rs1459704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471243	0.85[CHD][hapmap];1.00[GIH][hapmap]
rs17107547	0.83[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs17107592	0.82[ASN][1000 genomes]
rs17107610	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17175109	1.00[YRI][hapmap]
rs227416	0.95[GIH][hapmap]
rs227419	0.93[GIH][hapmap]
rs227425	1.00[GIH][hapmap]
rs227426	0.95[GIH][hapmap]
rs227437	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2281663	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs34311408	1.00[ASN][1000 genomes]
rs3825739	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs56031625	0.82[ASN][1000 genomes]
rs56242824	1.00[ASN][1000 genomes]
rs57609901	1.00[ASN][1000 genomes]
rs67294558	0.90[ASN][1000 genomes]
rs7141378	0.99[ASN][1000 genomes]
rs7151788	0.85[CHD][hapmap];1.00[GIH][hapmap]
rs7157226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7160726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8010305	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs8012912	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8015491	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs8016522	0.82[CHB][hapmap];0.82[CHD][hapmap]

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
rs12885683	SMOC1	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70457800-70484800	Weak transcription	Brain Substantia Nigra	brain
2	chr14:70458600-70480800	Weak transcription	Brain Germinal Matrix	brain
3	chr14:70459000-70484800	Weak transcription	Gastric	stomach
4	chr14:70466200-70484800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr14:70468400-70484400	Weak transcription	A549	lung
6	chr14:70469800-70484800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr14:70470400-70479800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr14:70472200-70481400	Weak transcription	Fetal Muscle Leg	muscle
9	chr14:70472400-70485400	Strong transcription	Hela-S3	cervix
10	chr14:70475200-70479200	Strong transcription	Liver	Liver
11	chr14:70475600-70478600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:70475600-70478600	Enhancers	HMEC	breast
13	chr14:70475800-70478400	Enhancers	NHEK	skin
14	chr14:70475800-70479000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr14:70475800-70480200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr14:70475800-70484800	Weak transcription	Brain Hippocampus Middle	brain
17	chr14:70475800-70487200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr14:70476000-70478400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr14:70476000-70480200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr14:70476000-70500000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr14:70476200-70478400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr14:70476200-70479800	Enhancers	GM12878-XiMat	blood
23	chr14:70476200-70480200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr14:70476200-70482200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr14:70476200-70490600	Weak transcription	Fetal Brain Male	brain
26	chr14:70476200-70499000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:70476600-70478400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr14:70476600-70480200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr14:70476600-70480600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr14:70477000-70479000	Strong transcription	HepG2	liver
31	chr14:70477000-70479200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr14:70477000-70479200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr14:70477000-70483000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr14:70477000-70484200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr14:70477200-70478600	Strong transcription	Spleen	Spleen
36	chr14:70477200-70478800	Strong transcription	Fetal Brain Female	brain
37	chr14:70477200-70480600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr14:70477400-70478800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr14:70477400-70484600	Weak transcription	Fetal Stomach	stomach

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