Variant report

Variant	rs13200559
Chromosome Location	chr6:56642320-56642321
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 145 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1024195	1.00[LWK][hapmap]
rs10498812	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10498813	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11756551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11968575	0.81[CEU][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap]
rs11970648	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs13190854	0.87[EUR][1000 genomes]
rs13192540	0.84[EUR][1000 genomes]
rs13192931	0.84[EUR][1000 genomes]
rs13194625	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13194904	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13195601	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13198204	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13198399	0.91[AMR][1000 genomes]
rs13198597	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs13198938	0.83[AMR][1000 genomes]
rs13200166	1.00[CEU][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13200768	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13200868	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13201639	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13201733	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13203000	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs13203148	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13203327	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13203681	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13204466	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13205667	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13207768	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs13208409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13211879	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13214135	0.81[AMR][1000 genomes]
rs13215883	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs13217390	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs13218913	1.00[CEU][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13219942	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs13220618	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13220628	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13220851	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1599280	1.00[ASW][hapmap]
rs1610157	0.82[EUR][1000 genomes]
rs16888171	1.00[CEU][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs16888186	0.87[CEU][hapmap]
rs17684730	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17684748	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17684772	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17684784	1.00[CEU][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684802	1.00[CEU][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17684878	1.00[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs17684884	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17685277	1.00[ASW][hapmap]
rs17751682	1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap]
rs17751695	1.00[MEX][hapmap]
rs17751966	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17751977	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17752002	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17752046	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17752106	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1903332	0.94[CEU][hapmap];0.84[TSI][hapmap]
rs28360570	0.80[EUR][1000 genomes]
rs3002007	0.80[EUR][1000 genomes]
rs3002010	0.81[CEU][hapmap]
rs3002011	0.80[CEU][hapmap]
rs34171958	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34228698	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34359353	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34425815	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34455199	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs34465210	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs34500949	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34520435	0.91[EUR][1000 genomes]
rs34566275	0.98[AMR][1000 genomes]
rs34587484	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs34612783	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34614087	0.87[EUR][1000 genomes]
rs34623351	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs34640766	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34803237	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs34832779	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34866877	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34896026	0.87[EUR][1000 genomes]
rs34966024	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35073881	0.84[EUR][1000 genomes]
rs35080938	0.83[EUR][1000 genomes]
rs35081015	0.88[EUR][1000 genomes]
rs35225175	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35242294	0.82[EUR][1000 genomes]
rs35251663	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35326806	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35407078	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35439100	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35440822	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35461301	0.87[EUR][1000 genomes]
rs35494794	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35566812	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35609883	0.92[EUR][1000 genomes]
rs35642890	0.92[EUR][1000 genomes]
rs35696739	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35828379	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35851452	0.87[EUR][1000 genomes]
rs35873865	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35876418	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs35886823	0.90[EUR][1000 genomes]
rs35986172	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs36022925	0.90[EUR][1000 genomes]
rs36037734	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36094082	0.84[EUR][1000 genomes]
rs4074101	1.00[MEX][hapmap]
rs41267675	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4299824	1.00[CEU][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4348308	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4371846	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4415160	1.00[CEU][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs4457154	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4532444	0.88[EUR][1000 genomes]
rs4587171	0.83[CEU][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs56368885	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58980183	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59432342	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61601344	0.95[EUR][1000 genomes]
rs62411366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62411367	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62411372	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62411375	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62411376	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6904535	1.00[EUR][1000 genomes]
rs6905603	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs6914293	0.82[EUR][1000 genomes]
rs6918949	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6928104	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6934714	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs71564854	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71564855	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71564856	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71564861	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71564863	0.84[EUR][1000 genomes]
rs7758867	1.00[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs7761501	1.00[CEU][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs7761729	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7771085	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7775182	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription 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 miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13200559	DST	cis	cerebellum	SCAN
rs13200559	BMP5	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56625600-56649800	Weak transcription	Brain Germinal Matrix	brain
2	chr6:56637800-56647200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:56638000-56650200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:56638000-56653000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:56638000-56654200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr6:56638000-56654400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:56638000-56654800	Weak transcription	Psoas Muscle	Psoas
8	chr6:56638000-56659200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:56638000-56659200	Weak transcription	NHLF	lung
10	chr6:56638200-56651200	Weak transcription	HSMMtube	muscle
11	chr6:56638400-56647800	Weak transcription	NH-A	brain
12	chr6:56638400-56655000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr6:56639400-56650000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:56640200-56642800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:56640400-56642400	Enhancers	Brain Substantia Nigra	brain
16	chr6:56640400-56643000	Enhancers	Brain Hippocampus Middle	brain
17	chr6:56640600-56642600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr6:56641000-56642400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:56641200-56642400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:56641200-56642600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr6:56641200-56642600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:56641200-56642600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr6:56641200-56642600	Strong transcription	HSMM	muscle
24	chr6:56641200-56643000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr6:56641200-56654800	Weak transcription	HUVEC	blood vessel
26	chr6:56641200-56659000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:56641600-56642400	Enhancers	Brain Angular Gyrus	brain
28	chr6:56641800-56642600	Enhancers	Brain Cingulate Gyrus	brain
29	chr6:56641800-56642600	Enhancers	Rectal Smooth Muscle	rectum
30	chr6:56642000-56642600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:56642200-56642400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:56642200-56642400	Enhancers	Colon Smooth Muscle	Colon
33	chr6:56642200-56642400	Enhancers	Right Atrium	heart
34	chr6:56642200-56642400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr6:56642200-56642600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:56642200-56642600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:56642200-56642600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:56642200-56642600	Weak transcription	Brain Anterior Caudate	brain
39	chr6:56642200-56642600	Enhancers	A549	lung
40	chr6:56642200-56642800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr6:56642200-56642800	Enhancers	H9 Cell Line	embryonic stem cell
42	chr6:56642200-56642800	Enhancers	Left Ventricle	heart

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