Variant report

Variant	rs10139615
Chromosome Location	chr14:70403529-70403530
allele	A/G
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: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10151432	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs190133	0.80[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs227388	0.80[TSI][hapmap]
rs227396	0.84[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs227398	0.89[GIH][hapmap];0.80[MEX][hapmap]
rs227428	0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs227432	0.95[CHB][hapmap]
rs7142820	0.95[CHB][hapmap]
rs7148010	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs7159801	0.89[CHB][hapmap]
rs8003679	0.87[CHD][hapmap]
rs8016072	0.95[CHB][hapmap];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10139615	FAM71D	cis	cerebellum	SCAN
rs10139615	PCNX	cis	cerebellum	SCAN
rs10139615	SMOC1	cis	Artery Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70395200-70404200	Weak transcription	Spleen	Spleen
2	chr14:70395600-70404400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr14:70396000-70404200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr14:70397400-70406400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr14:70398400-70409400	Enhancers	Liver	Liver
6	chr14:70399400-70407200	Weak transcription	Brain Substantia Nigra	brain
7	chr14:70399600-70406400	Strong transcription	Hela-S3	cervix
8	chr14:70399600-70409600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:70400200-70404800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr14:70402200-70403800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr14:70402400-70403600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:70402400-70404000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
13	chr14:70402800-70404200	Enhancers	HepG2	liver
14	chr14:70402800-70405400	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:70403000-70403600	Enhancers	HMEC	breast
16	chr14:70403000-70404400	Enhancers	Placenta	Placenta
17	chr14:70403000-70404800	Enhancers	Pancreas	Pancrea
18	chr14:70403000-70406600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:70403400-70404200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr14:70403400-70404400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr14:70403400-70404400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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