Variant report

Variant	rs12526227
Chromosome Location	chr6:76563877-76563878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10806048	0.83[AMR][1000 genomes]
rs10943292	0.88[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs11970551	0.83[AMR][1000 genomes]
rs12209903	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12662659	0.83[AMR][1000 genomes]
rs1322551	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1358954	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1407510	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1535501	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2004170	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2181245	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2181246	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273859	0.86[GIH][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes]
rs2312940	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2647404	0.90[JPT][hapmap]
rs2748959	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2748964	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2842538	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2842540	0.86[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2842542	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2842544	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2842546	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2842549	0.86[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3798447	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3798448	0.82[AMR][1000 genomes]
rs6934542	0.83[AMR][1000 genomes]
rs699186	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs720862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs720863	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72890648	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9294005	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9443195	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9447579	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022428	chr6:76023118-76575620	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv538312	chr6:76023118-76575620	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
3	nsv1019328	chr6:76154751-76604197	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv538314	chr6:76154751-76604197	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
5	nsv1021090	chr6:76306100-76759397	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv538318	chr6:76306100-76759397	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv1032961	chr6:76343575-76788852	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv932201	chr6:76365548-77219650	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1028340	chr6:76410921-76960225	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	nsv538319	chr6:76410921-76960225	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12526227	SENP6	cis	parietal	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76520200-76576400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr6:76521800-76571000	Weak transcription	Gastric	stomach
3	chr6:76523800-76569000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:76534200-76572400	Weak transcription	Brain Anterior Caudate	brain
5	chr6:76539400-76572400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:76541000-76590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:76541200-76572600	Weak transcription	HSMMtube	muscle
8	chr6:76541400-76572400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:76543000-76568800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:76543000-76569200	Weak transcription	Lung	lung
11	chr6:76543000-76615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:76543200-76566600	Weak transcription	HMEC	breast
13	chr6:76544000-76583200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:76544200-76572600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:76544400-76572600	Weak transcription	Aorta	Aorta
16	chr6:76544400-76572600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:76544400-76603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr6:76545800-76566800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:76547400-76572600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:76551000-76565600	Weak transcription	Liver	Liver
21	chr6:76551200-76566800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:76551200-76567200	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:76551200-76572600	Weak transcription	Placenta	Placenta
24	chr6:76552000-76566800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:76552000-76571200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr6:76552200-76567400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:76552200-76569000	Weak transcription	Adipose Nuclei	Adipose
28	chr6:76552200-76572400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:76552200-76592400	Weak transcription	HSMM	muscle
30	chr6:76552600-76592400	Weak transcription	Psoas Muscle	Psoas
31	chr6:76553200-76564800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:76553400-76572600	Weak transcription	Brain Angular Gyrus	brain
33	chr6:76554200-76572400	Weak transcription	Brain Substantia Nigra	brain
34	chr6:76559200-76565600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:76559600-76576000	Weak transcription	Left Ventricle	heart
36	chr6:76560000-76568200	Weak transcription	Fetal Stomach	stomach
37	chr6:76560000-76572200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:76560000-76572600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:76560000-76585800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:76560200-76567400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:76560200-76571200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:76560400-76567200	Weak transcription	Fetal Kidney	kidney
43	chr6:76560400-76572600	Weak transcription	NH-A	brain
44	chr6:76560400-76572600	Weak transcription	NHEK	skin
45	chr6:76560400-76583200	Weak transcription	Osteobl	bone
46	chr6:76560600-76565000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:76560600-76571600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:76560600-76572600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:76561600-76566600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr6:76561600-76569000	Weak transcription	Pancreas	Pancrea

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