Variant report

Variant	rs190133
Chromosome Location	chr14:70404674-70404675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:69618958..69620849-chr14:70403396..70405755,2	MCF-7	breast:
2	chr14:70402768..70405371-chr14:70458145..70461044,2	MCF-7	breast:
3	chr14:70403462..70405160-chr14:70409353..70411324,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198732	Chromatin interaction
ENSG00000139990	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10139615	0.80[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs1276114	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1276115	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1276116	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1276120	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs1276121	0.91[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs1314983	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1951510	0.86[ASN][1000 genomes]
rs227388	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227395	0.86[CHD][hapmap]
rs227396	0.96[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs227397	0.88[CHD][hapmap];0.85[GIH][hapmap]
rs227398	0.88[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap]
rs927414	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs962959	0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs190133	SMOC1	cis	Artery Tibial	GTEx
rs190133	FAM71D	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70397400-70406400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr14:70398400-70409400	Enhancers	Liver	Liver
3	chr14:70399400-70407200	Weak transcription	Brain Substantia Nigra	brain
4	chr14:70399600-70406400	Strong transcription	Hela-S3	cervix
5	chr14:70399600-70409600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr14:70400200-70404800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:70402800-70405400	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:70403000-70404800	Enhancers	Pancreas	Pancrea
9	chr14:70403000-70406600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr14:70403600-70411600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr14:70403800-70404800	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr14:70403800-70406400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr14:70404000-70405000	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr14:70404200-70404800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr14:70404200-70404800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr14:70404200-70404800	Flanking Active TSS	HepG2	liver
17	chr14:70404200-70405200	Enhancers	Fetal Brain Male	brain
18	chr14:70404400-70405400	Weak transcription	Placenta	Placenta
19	chr14:70404400-70405600	Enhancers	Fetal Stomach	stomach
20	chr14:70404400-70405800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr14:70404400-70405800	Enhancers	Gastric	stomach
22	chr14:70404600-70404800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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