Variant report

Variant	rs10139666
Chromosome Location	chr14:39493157-39493158
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10129762	0.87[EUR][1000 genomes]
rs10134166	0.85[EUR][1000 genomes]
rs10134656	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10135561	0.92[GIH][hapmap];0.86[MEX][hapmap]
rs10141079	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10141081	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10142117	0.82[EUR][1000 genomes]
rs10148712	0.92[GIH][hapmap]
rs10150756	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10151124	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10151960	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1040680	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10483543	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050136	0.86[MEX][hapmap]
rs11622731	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11623907	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11623945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11625689	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11627264	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11628480	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11628564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11628784	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11845793	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11848067	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12323565	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12587208	0.92[GIH][hapmap];0.88[MEX][hapmap]
rs12590373	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13021	0.92[GIH][hapmap];0.86[MEX][hapmap]
rs17092044	0.87[EUR][1000 genomes]
rs17108596	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17108664	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17108696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1884384	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs2025061	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2144528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28414518	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28470602	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28821293	0.85[EUR][1000 genomes]
rs3896147	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55672305	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55737943	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56064304	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56105133	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56785762	0.82[ASN][1000 genomes]
rs57326310	0.87[EUR][1000 genomes]
rs57482489	0.85[EUR][1000 genomes]
rs58601678	0.85[EUR][1000 genomes]
rs59465524	0.85[EUR][1000 genomes]
rs7144625	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7159520	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs743223	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8019396	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs926970	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs993675	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10139666	MIPOL1	cis	parietal	SCAN
rs10139666	BRMS1L	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39463600-39495200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr14:39465600-39498200	Weak transcription	NH-A	brain
3	chr14:39469200-39497400	Weak transcription	HSMM	muscle
4	chr14:39473400-39498800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:39479600-39498000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr14:39480200-39499000	Weak transcription	NHDF-Ad	bronchial
7	chr14:39482200-39495000	Weak transcription	HUVEC	blood vessel
8	chr14:39482800-39499200	Weak transcription	Right Ventricle	heart
9	chr14:39485200-39498600	Weak transcription	Aorta	Aorta
10	chr14:39486000-39498600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr14:39486400-39495400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr14:39486400-39497400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:39486400-39498600	Weak transcription	HSMMtube	muscle
14	chr14:39486600-39498600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr14:39486800-39495200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr14:39486800-39495200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr14:39486800-39498800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr14:39487000-39498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr14:39487000-39499400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr14:39487200-39498600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr14:39487200-39498600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr14:39487200-39508600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr14:39491400-39499200	Weak transcription	NHEK	skin
24	chr14:39492000-39498800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr14:39492600-39493400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr14:39492600-39494400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr14:39492600-39495400	Strong transcription	Osteobl	bone
28	chr14:39492600-39495600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr14:39492600-39496400	Enhancers	Fetal Intestine Large	intestine
30	chr14:39492600-39496400	Enhancers	Fetal Intestine Small	intestine
31	chr14:39492600-39498800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr14:39492800-39493200	Enhancers	Fetal Brain Female	brain
33	chr14:39492800-39493400	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr14:39492800-39493600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr14:39492800-39493600	Enhancers	HMEC	breast
36	chr14:39492800-39494400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr14:39492800-39495800	Enhancers	Stomach Mucosa	stomach
38	chr14:39492800-39495800	Flanking Active TSS	HepG2	liver
39	chr14:39492800-39496400	Enhancers	Liver	Liver
40	chr14:39493000-39493200	Enhancers	A549	lung
41	chr14:39493000-39493400	Enhancers	Duodenum Mucosa	Duodenum
42	chr14:39493000-39494000	Weak transcription	Pancreas	Pancrea
43	chr14:39493000-39494000	Weak transcription	Small Intestine	intestine
44	chr14:39493000-39498000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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