Variant report

Variant	rs13202519
Chromosome Location	chr6:76584271-76584272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12664049	0.93[CHB][hapmap]
rs1280049	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1280050	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1280051	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1280052	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1280053	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1280054	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]
rs1280055	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1280056	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1280057	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1280058	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1322549	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34090650	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3778007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3798425	0.94[CHB][hapmap];0.94[CHD][hapmap];0.80[ASN][1000 genomes]
rs3798426	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798429	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798433	0.94[CHB][hapmap];0.94[CHD][hapmap]
rs4476795	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]
rs6914716	0.89[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.94[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6924528	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6932992	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7742567	1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7767675	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910679	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9341539	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9343325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9343327	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9359141	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9359147	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9360954	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9766905	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
rs13202519	SENP6	cis	parietal	SCAN
rs13202519	MYO6	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76541000-76590600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr6:76543000-76615000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:76544400-76603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:76552200-76592400	Weak transcription	HSMM	muscle
5	chr6:76552600-76592400	Weak transcription	Psoas Muscle	Psoas
6	chr6:76560000-76585800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:76562400-76599800	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:76563000-76585400	Weak transcription	NHDF-Ad	bronchial
9	chr6:76563400-76602800	Weak transcription	Small Intestine	intestine
10	chr6:76566200-76604600	Weak transcription	Right Ventricle	heart
11	chr6:76567000-76604400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:76567600-76598600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:76567600-76604200	Weak transcription	NHLF	lung
14	chr6:76571200-76592400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:76573000-76597800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:76573000-76624000	Weak transcription	Placenta	Placenta
17	chr6:76573200-76604200	Weak transcription	Colonic Mucosa	Colon
18	chr6:76573400-76592800	Weak transcription	Stomach Mucosa	stomach
19	chr6:76573600-76606200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:76573800-76607200	Weak transcription	Gastric	stomach
21	chr6:76573800-76608400	Weak transcription	Esophagus	oesophagus
22	chr6:76574000-76584600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:76574400-76632600	Weak transcription	Spleen	Spleen
24	chr6:76575600-76586400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:76576000-76604000	Weak transcription	Fetal Brain Female	brain
26	chr6:76577200-76585600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:76577200-76624600	Weak transcription	Fetal Kidney	kidney
28	chr6:76577400-76587800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:76577400-76591800	Weak transcription	NHEK	skin
30	chr6:76577400-76592000	Weak transcription	HMEC	breast
31	chr6:76577400-76594000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:76580000-76591600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:76580200-76586600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:76580600-76591800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:76580800-76585400	Strong transcription	Fetal Intestine Small	intestine
36	chr6:76581000-76594800	Strong transcription	Fetal Intestine Large	intestine
37	chr6:76582000-76593200	Weak transcription	Fetal Brain Male	brain
38	chr6:76582200-76586400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:76582400-76584800	Weak transcription	Brain Germinal Matrix	brain
40	chr6:76582400-76585200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:76582600-76584800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:76582600-76584800	Strong transcription	Brain Anterior Caudate	brain
43	chr6:76582600-76586400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:76582800-76584400	Strong transcription	HSMMtube	muscle
45	chr6:76582800-76584800	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr6:76582800-76585800	Strong transcription	Adipose Nuclei	Adipose
47	chr6:76582800-76585800	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr6:76582800-76586400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:76582800-76586400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:76583000-76585800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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