Variant report

Variant	rs227429
Chromosome Location	chr14:70390756-70390757
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	chr14:70390089..70391707-chr14:70394877..70397493,2	MCF-7	breast:
2	chr14:70389062..70391123-chr14:70393251..70396818,3	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1007695	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1275842	1.00[CHD][hapmap]
rs1275843	1.00[CHD][hapmap]
rs1295832	1.00[CHD][hapmap]
rs17107753	1.00[CHD][hapmap]
rs17107766	1.00[CHD][hapmap]
rs17174862	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1903201	1.00[CHD][hapmap]
rs227404	1.00[CHD][hapmap]
rs227430	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2766463	1.00[CHD][hapmap]
rs7151975	1.00[CHD][hapmap]
rs7155412	1.00[JPT][hapmap]
rs8008770	1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs227429	FAM71D	cis	parietal	SCAN
rs227429	SNORD56B	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70377800-70394400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:70384800-70394400	Weak transcription	HepG2	liver
3	chr14:70387600-70390800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr14:70387600-70391800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr14:70389000-70396800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr14:70389200-70394400	Weak transcription	Brain Germinal Matrix	brain
7	chr14:70389400-70391000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr14:70389400-70391000	Weak transcription	Osteobl	bone
9	chr14:70389400-70393800	Weak transcription	Spleen	Spleen
10	chr14:70389400-70394400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr14:70389400-70394400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr14:70389600-70390800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:70389600-70390800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr14:70390200-70391000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:70390200-70391000	Strong transcription	Liver	Liver
16	chr14:70390200-70391200	Strong transcription	Hela-S3	cervix
17	chr14:70390200-70391400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr14:70390200-70391400	Enhancers	Brain Cingulate Gyrus	brain
19	chr14:70390400-70391400	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr14:70390400-70391400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr14:70390400-70391600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr14:70390600-70391000	Enhancers	Brain Hippocampus Middle	brain
23	chr14:70390600-70391000	Enhancers	Brain Substantia Nigra	brain
24	chr14:70390600-70391000	Bivalent Enhancer	Fetal Stomach	stomach
25	chr14:70390600-70391200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
26	chr14:70390600-70391400	Enhancers	Placenta	Placenta

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