Variant report

Variant	rs12883884
Chromosome Location	chr14:70517183-70517184
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10129447	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142899	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1122271	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs11629291	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12435978	0.91[CHD][hapmap]
rs2125744	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs227434	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs2839867	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809401	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.84[ASN][1000 genomes]
rs4899323	0.81[CHD][hapmap]
rs4902771	0.81[CHD][hapmap]
rs7141091	0.88[CHD][hapmap]
rs7142759	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8014694	0.91[CHD][hapmap]
rs998919	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Cystic fibrosis severity	21602797	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12883884	SMOC1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70511200-70518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr14:70511600-70519000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr14:70512800-70535600	Weak transcription	Psoas Muscle	Psoas
4	chr14:70513200-70519200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr14:70513200-70520000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:70514200-70518000	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr14:70514600-70531200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr14:70514800-70517800	Enhancers	HepG2	liver
9	chr14:70515800-70520000	Weak transcription	Fetal Brain Female	brain
10	chr14:70516000-70518800	Weak transcription	Gastric	stomach
11	chr14:70516400-70517200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:70516400-70517200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr14:70516400-70517800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr14:70516600-70517800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:70516600-70518000	Strong transcription	HSMMtube	muscle
16	chr14:70517000-70517200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr14:70517000-70517200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr14:70517000-70517800	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr14:70517000-70525200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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