Variant report

Variant	rs1460561
Chromosome Location	chr6:56797574-56797575
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56795022..56797639-chr6:56802844..56804905,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1044670	1.00[ASW][hapmap]
rs13193465	0.85[GIH][hapmap]
rs13195825	0.93[AFR][1000 genomes]
rs13198484	0.93[AFR][1000 genomes]
rs13203600	0.93[AFR][1000 genomes]
rs13205022	0.93[AFR][1000 genomes]
rs13207768	1.00[ASW][hapmap]
rs13209099	0.93[AFR][1000 genomes]
rs13214032	1.00[AFR][1000 genomes]
rs13215865	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13216793	0.93[AFR][1000 genomes]
rs13220510	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13220575	0.85[GIH][hapmap]
rs1451707	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1451708	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1599280	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1599281	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17450853	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17685143	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17685185	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17685277	1.00[ASW][hapmap];0.85[GIH][hapmap];0.87[LWK][hapmap];1.00[AFR][1000 genomes]
rs17685338	1.00[AFR][1000 genomes]
rs17685380	1.00[AFR][1000 genomes]
rs17752412	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17752435	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17752459	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1903330	1.00[CEU][hapmap];0.85[LWK][hapmap];0.96[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2817573	0.85[GIH][hapmap]
rs28360537	1.00[AFR][1000 genomes]
rs28360538	1.00[AFR][1000 genomes]
rs34009699	1.00[AFR][1000 genomes]
rs34027274	1.00[AFR][1000 genomes]
rs34232358	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34259328	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34399458	1.00[AFR][1000 genomes]
rs34616943	1.00[AFR][1000 genomes]
rs34714091	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34733863	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs34752771	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34812189	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35202312	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35434542	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35527216	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35860642	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35961728	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36112505	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3957366	1.00[ASW][hapmap]
rs4490669	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55786720	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56030203	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58338781	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61340009	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6901944	0.85[GIH][hapmap]
rs71550519	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564866	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71564868	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs720884	1.00[ASW][hapmap];0.85[GIH][hapmap];0.87[LWK][hapmap];1.00[AFR][1000 genomes]
rs748996	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7760385	1.00[AFR][1000 genomes]
rs9296855	0.82[TSI][hapmap]
rs9475752	1.00[CEU][hapmap];0.98[EUR][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	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
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv5315	chr6:56752042-56798761	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1460561	RAB23	cis	multi-tissue	Pritchard
rs1460561	BEND6	cis	parietal	SCAN
rs1460561	DST	cis	cerebellum	SCAN
rs1460561	BEND6	cis	cerebellum	SCAN
rs1460561	BEND6	cis	Artery Tibial	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56790400-56799800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:56792800-56802400	Weak transcription	A549	lung
3	chr6:56793000-56802600	Weak transcription	HSMM	muscle
4	chr6:56793200-56798000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:56793200-56798200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:56793200-56799000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:56793200-56799800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:56793200-56802600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:56793200-56803000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:56793200-56803000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:56793200-56803000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:56793200-56803200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:56793400-56798200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:56795000-56797800	Weak transcription	Hela-S3	cervix
15	chr6:56796000-56799600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:56796200-56803800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:56796800-56803800	Weak transcription	HSMMtube	muscle
18	chr6:56797000-56797800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:56797000-56798200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:56797000-56798800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:56797200-56797600	Strong transcription	NHLF	lung
22	chr6:56797200-56797800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:56797200-56797800	Enhancers	GM12878-XiMat	blood
24	chr6:56797200-56798200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:56797200-56798400	Strong transcription	Osteobl	bone
26	chr6:56797400-56797600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr6:56797400-56798200	Strong transcription	NHDF-Ad	bronchial
28	chr6:56797400-56798800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr6:56797400-56799200	Enhancers	Primary hematopoietic stem cells	blood

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