Variant report

Variant	rs227437
Chromosome Location	chr14:70454272-70454273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10134291	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs10134965	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11158827	0.83[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12050076	0.84[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12050089	0.90[ASN][1000 genomes]
rs12101270	0.94[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12433177	1.00[GIH][hapmap]
rs12878947	0.90[ASN][1000 genomes]
rs12885068	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12885683	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12887943	0.94[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12889195	0.90[ASN][1000 genomes]
rs12890357	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1459704	0.83[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs17107547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17107592	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17107610	0.83[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs192024	0.81[CHD][hapmap]
rs227412	0.84[CHD][hapmap];1.00[GIH][hapmap]
rs227416	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs227419	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs227420	0.82[ASN][1000 genomes]
rs227422	0.83[ASN][1000 genomes]
rs227423	0.83[ASN][1000 genomes]
rs227424	0.81[ASN][1000 genomes]
rs227425	0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs227426	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs227427	0.81[ASN][1000 genomes]
rs227438	0.81[ASN][1000 genomes]
rs227439	0.81[ASN][1000 genomes]
rs34311408	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3825739	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56031625	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56242824	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57609901	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60011612	0.84[AMR][1000 genomes]
rs61305	0.84[CHD][hapmap];1.00[GIH][hapmap];0.82[ASN][1000 genomes]
rs67294558	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7141378	0.89[ASN][1000 genomes]
rs7157226	0.83[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7160726	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs8012912	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs8015491	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs227437	SMOC1	cis	parietal	SCAN
rs227437	MAP3K9	cis	intralobular white matter	BrainEAC
rs227437	GALNTL1	cis	parietal	SCAN

Chromatin state (count:40 , 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	chr14:70447000-70454400	Genic enhancers	Hela-S3	cervix
4	chr14:70447600-70454400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:70448200-70455000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr14:70450000-70458600	Weak transcription	Aorta	Aorta
7	chr14:70450600-70456400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:70450600-70457000	Weak transcription	Fetal Brain Male	brain
9	chr14:70450600-70464800	Weak transcription	Fetal Stomach	stomach
10	chr14:70450600-70477200	Weak transcription	Fetal Brain Female	brain
11	chr14:70451800-70459200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr14:70452400-70458400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr14:70452800-70454600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr14:70452800-70460600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr14:70453000-70464800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr14:70453200-70457800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:70453200-70458600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr14:70453200-70462600	Weak transcription	NHEK	skin
19	chr14:70453400-70454600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:70453400-70454600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr14:70453400-70455000	Enhancers	Brain Hippocampus Middle	brain
22	chr14:70453400-70455200	Enhancers	Brain Substantia Nigra	brain
23	chr14:70453600-70454600	Enhancers	Brain Germinal Matrix	brain
24	chr14:70453600-70455000	Enhancers	Brain Cingulate Gyrus	brain
25	chr14:70453600-70455200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr14:70453600-70456400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr14:70453600-70462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:70453800-70454600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr14:70453800-70454600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr14:70453800-70455000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr14:70453800-70455000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr14:70453800-70455400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr14:70454000-70454400	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr14:70454000-70454400	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr14:70454000-70455800	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr14:70454000-70455800	Weak transcription	Liver	Liver
37	chr14:70454000-70455800	Weak transcription	HepG2	liver
38	chr14:70454000-70456400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr14:70454200-70454600	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr14:70454200-70457400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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