Variant report

Variant	rs227425
Chromosome Location	chr14:70456699-70456700
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:70456314-70457005	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr14:70456335-70461656	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr14:70456315-70459260	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70405053..70407734-chr14:70454995..70457113,2	MCF-7	breast:

Variant related genes	Relation type
SMOC1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10134291	1.00[GIH][hapmap]
rs10134965	1.00[GIH][hapmap]
rs11158827	0.95[GIH][hapmap]
rs12050076	0.80[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12433177	0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12885683	1.00[GIH][hapmap]
rs1471243	0.80[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs17107547	0.83[ASN][1000 genomes]
rs17107592	0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs17107610	1.00[GIH][hapmap]
rs182745	0.86[CHD][hapmap]
rs192024	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs227412	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs227416	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs227417	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs227419	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[ASN][1000 genomes]
rs227420	0.99[ASN][1000 genomes]
rs227422	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs227423	1.00[ASN][1000 genomes]
rs227424	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs227426	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs227427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs227437	0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs227438	0.81[CHB][hapmap];0.99[ASN][1000 genomes]
rs227439	0.99[ASN][1000 genomes]
rs227444	0.91[JPT][hapmap]
rs56031625	0.90[ASN][1000 genomes]
rs61305	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs67294558	0.83[ASN][1000 genomes]
rs7151788	0.80[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs8012912	0.95[GIH][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

Variant related diseases (count:1)

Disease	PMID	Source
Bone mineral density	24249740	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs227425	SMOC1	cis	Artery Tibial	GTEx
rs227425	FAM71D	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70439000-70458800	Weak transcription	Gastric	stomach
2	chr14:70439800-70477200	Weak transcription	Spleen	Spleen
3	chr14:70450000-70458600	Weak transcription	Aorta	Aorta
4	chr14:70450600-70457000	Weak transcription	Fetal Brain Male	brain
5	chr14:70450600-70464800	Weak transcription	Fetal Stomach	stomach
6	chr14:70450600-70477200	Weak transcription	Fetal Brain Female	brain
7	chr14:70451800-70459200	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr14:70452400-70458400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr14:70452800-70460600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr14:70453000-70464800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr14:70453200-70457800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:70453200-70458600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr14:70453200-70462600	Weak transcription	NHEK	skin
14	chr14:70453600-70462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr14:70454200-70457400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr14:70454600-70458600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr14:70454800-70460800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr14:70455800-70457400	Enhancers	HepG2	liver
19	chr14:70455800-70458600	Enhancers	Liver	Liver
20	chr14:70456200-70457400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr14:70456400-70456800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr14:70456400-70456800	Enhancers	Pancreas	Pancrea
23	chr14:70456400-70457000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr14:70456400-70457800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:70456400-70457800	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr14:70456400-70458600	Enhancers	Brain Germinal Matrix	brain
27	chr14:70456400-70459200	Enhancers	Brain Hippocampus Middle	brain
28	chr14:70456600-70456800	Enhancers	Brain Anterior Caudate	brain
29	chr14:70456600-70457000	Enhancers	Hela-S3	cervix
30	chr14:70456600-70457600	Enhancers	Brain Cingulate Gyrus	brain
31	chr14:70456600-70457800	Enhancers	Brain Substantia Nigra	brain

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