Variant report

Variant	rs699186
Chromosome Location	chr6:76625079-76625080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:76613924..76617174-chr6:76621064..76625151,5	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10806048	0.84[EUR][1000 genomes]
rs10943292	0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs11970551	0.84[EUR][1000 genomes]
rs12209903	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12526227	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]
rs12662659	0.84[EUR][1000 genomes]
rs1322551	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1358954	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1407510	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1535501	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2004170	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2181245	0.96[CEU][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2181246	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs2273859	0.96[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2312940	0.82[ASN][1000 genomes]
rs2647404	0.90[JPT][hapmap]
rs2748959	0.82[EUR][1000 genomes]
rs2748964	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2842538	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2842540	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2842542	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2842544	0.82[EUR][1000 genomes]
rs2842546	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2842549	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs3798447	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3798448	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6934542	0.84[EUR][1000 genomes]
rs720862	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs720863	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72890648	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9294005	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9443195	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9447579	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs699186	MYO6	cis	cerebellum	SCAN
rs699186	SENP6	cis	parietal	SCAN
rs699186	TMEM30A	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:76574400-76632600	Weak transcription	Spleen	Spleen
2	chr6:76584200-76629400	Weak transcription	Ovary	ovary
3	chr6:76584800-76644600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:76585800-76626800	Weak transcription	Left Ventricle	heart
5	chr6:76585800-76644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:76586000-76627600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:76592800-76631800	Weak transcription	NHEK	skin
8	chr6:76594600-76632200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:76600200-76631800	Weak transcription	HMEC	breast
10	chr6:76604400-76627000	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:76606600-76628800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:76606600-76629200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:76606600-76632000	Weak transcription	NHDF-Ad	bronchial
14	chr6:76606800-76632000	Weak transcription	HSMM	muscle
15	chr6:76608600-76628000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:76608600-76629400	Weak transcription	Aorta	Aorta
17	chr6:76615200-76628400	Weak transcription	Fetal Intestine Small	intestine
18	chr6:76615800-76630200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:76616000-76626800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:76616200-76627000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:76617200-76631600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:76617600-76626400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:76617600-76626600	Weak transcription	Fetal Heart	heart
24	chr6:76619400-76626600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:76620600-76644400	Weak transcription	HUVEC	blood vessel
26	chr6:76621000-76629200	Weak transcription	Fetal Stomach	stomach
27	chr6:76621600-76632200	Weak transcription	Right Ventricle	heart
28	chr6:76622000-76640400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:76622600-76633800	Weak transcription	Small Intestine	intestine
30	chr6:76622800-76630600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr6:76622800-76631600	Weak transcription	Colonic Mucosa	Colon
32	chr6:76622800-76632000	Weak transcription	NHLF	lung
33	chr6:76623000-76625400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:76623000-76625600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:76623000-76627400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr6:76623200-76644600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr6:76623600-76625400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:76623600-76626200	Weak transcription	HSMMtube	muscle
39	chr6:76623600-76631400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:76623800-76625200	Strong transcription	Brain Anterior Caudate	brain
41	chr6:76623800-76625600	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr6:76623800-76626600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr6:76623800-76627000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:76623800-76628400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:76623800-76630200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr6:76623800-76630400	Strong transcription	Adipose Nuclei	Adipose
47	chr6:76623800-76644400	Weak transcription	Stomach Mucosa	stomach
48	chr6:76624000-76625200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr6:76624000-76627200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:76624000-76630200	Strong transcription	Liver	Liver

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