Variant report

Variant	rs1280054
Chromosome Location	chr6:76540988-76540989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10498904	0.85[CHB][hapmap];0.83[CHD][hapmap]
rs10943294	0.88[AFR][1000 genomes]
rs10943295	0.88[AFR][1000 genomes]
rs11755704	0.85[CHB][hapmap]
rs11758543	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs12153964	0.83[AFR][1000 genomes]
rs12196105	0.81[LWK][hapmap]
rs12197993	0.85[AFR][1000 genomes]
rs12203461	0.92[LWK][hapmap];0.88[AFR][1000 genomes]
rs12210386	0.92[LWK][hapmap];0.88[AFR][1000 genomes]
rs12210963	0.85[LWK][hapmap];0.83[AFR][1000 genomes]
rs12211173	0.88[AFR][1000 genomes]
rs12211735	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs12212604	0.88[AFR][1000 genomes]
rs12216518	0.96[LWK][hapmap];0.88[AFR][1000 genomes]
rs12606	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs1280038	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs1280040	0.85[CHB][hapmap]
rs1280049	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1280050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280051	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1280052	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1280053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280055	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1280056	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1280057	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1280058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193694	0.81[AFR][1000 genomes]
rs13202519	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13204537	0.81[AFR][1000 genomes]
rs13216921	0.85[LWK][hapmap]
rs1322549	0.89[EUR][1000 genomes]
rs1335043	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17189990	0.85[CHB][hapmap]
rs17191306	0.85[CHB][hapmap]
rs17192223	0.85[CHB][hapmap]
rs17192279	0.85[CHB][hapmap]
rs17414086	0.85[CHB][hapmap]
rs17414687	0.85[CHB][hapmap]
rs17414729	0.85[CHB][hapmap]
rs17414757	0.85[CHB][hapmap]
rs17499394	0.85[CHB][hapmap]
rs17499531	0.85[CHB][hapmap]
rs17792195	0.85[CHB][hapmap]
rs17794529	0.82[CHB][hapmap]
rs17800625	0.85[CHB][hapmap]
rs2104203	0.85[CHB][hapmap]
rs2295936	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs2748957	0.85[CHB][hapmap]
rs276695	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs2842541	0.85[CHB][hapmap]
rs28619506	0.94[ASN][1000 genomes]
rs34090650	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3765140	0.85[CHB][hapmap]
rs3778007	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3798426	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3798427	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3798429	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3798434	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs3798435	0.85[CHB][hapmap]
rs3798440	0.96[LWK][hapmap];0.88[AFR][1000 genomes]
rs3798441	0.96[LWK][hapmap];0.88[AFR][1000 genomes]
rs3798442	0.83[AFR][1000 genomes]
rs3798455	0.81[LWK][hapmap]
rs4476795	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6914716	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6924528	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6932992	0.89[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs766244	0.85[CHB][hapmap]
rs7742567	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7767675	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7775832	0.85[CHB][hapmap]
rs910679	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9250	0.85[CHB][hapmap]
rs9341539	0.92[CEU][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9343325	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9343327	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9350602	0.96[LWK][hapmap];0.85[AFR][1000 genomes]
rs9352244	0.96[LWK][hapmap]
rs9359141	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9360946	0.85[LWK][hapmap]
rs9360954	0.92[CEU][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs956653	0.85[CHB][hapmap]
rs9766905	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs999209	0.85[CHB][hapmap];0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1032245	chr6:76045537-76545703	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv538313	chr6:76045537-76545703	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1280054	MYO6	cis	cerebellum	SCAN
rs1280054	SENP6	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76519400-76542600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr6:76520200-76576400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr6:76521200-76542600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:76521200-76542800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:76521400-76546200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:76521400-76547600	Weak transcription	Colonic Mucosa	Colon
7	chr6:76521800-76571000	Weak transcription	Gastric	stomach
8	chr6:76522000-76558800	Weak transcription	Ovary	ovary
9	chr6:76522200-76542600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:76522200-76554200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:76522600-76559000	Weak transcription	Fetal Kidney	kidney
12	chr6:76523800-76541200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:76523800-76542600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:76523800-76542800	Weak transcription	Lung	lung
15	chr6:76523800-76569000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:76524000-76541000	Weak transcription	Fetal Stomach	stomach
17	chr6:76524000-76542600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:76524000-76542800	Weak transcription	Esophagus	oesophagus
19	chr6:76524000-76543000	Weak transcription	Brain Substantia Nigra	brain
20	chr6:76524000-76544000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:76524200-76542600	Weak transcription	Brain Angular Gyrus	brain
22	chr6:76524400-76542800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:76525600-76550200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:76527200-76558800	Weak transcription	Small Intestine	intestine
25	chr6:76528200-76542600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:76528400-76550400	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:76528600-76542600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:76528600-76542600	Weak transcription	HUVEC	blood vessel
29	chr6:76528600-76548400	Weak transcription	NHLF	lung
30	chr6:76532800-76553000	Weak transcription	HepG2	liver
31	chr6:76533000-76542600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr6:76533200-76559400	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:76533800-76542600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:76534200-76541600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:76534200-76572400	Weak transcription	Brain Anterior Caudate	brain
36	chr6:76534400-76556600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:76535400-76541000	Weak transcription	Fetal Intestine Small	intestine
38	chr6:76536200-76552000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr6:76538200-76559200	Weak transcription	Pancreas	Pancrea
40	chr6:76538400-76542800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:76539400-76541200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:76539400-76572400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:76539600-76541000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:76539600-76544400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:76540200-76541200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:76540200-76542600	Weak transcription	Placenta	Placenta
47	chr6:76540200-76544200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr6:76540200-76544800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr6:76540400-76541200	Strong transcription	Adipose Nuclei	Adipose
50	chr6:76540400-76541200	Enhancers	HSMMtube	muscle

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