Variant report

Variant	rs1599281
Chromosome Location	chr6:56789311-56789312
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56785340..56787401-chr6:56789206..56791573,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11963379	1.00[ASN][1000 genomes]
rs12214882	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13193465	1.00[GIH][hapmap]
rs13215865	0.81[EUR][1000 genomes]
rs13220510	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13220575	1.00[GIH][hapmap]
rs1451707	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1451708	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1460561	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1599280	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17450853	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685143	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17685185	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17685277	1.00[GIH][hapmap]
rs17752412	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752435	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17752459	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1903330	1.00[CEU][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2817573	1.00[GIH][hapmap]
rs34232358	0.81[EUR][1000 genomes]
rs34259328	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34714091	0.81[EUR][1000 genomes]
rs34733863	0.82[EUR][1000 genomes]
rs34752771	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34812189	0.90[EUR][1000 genomes]
rs35202312	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35301163	0.86[AFR][1000 genomes]
rs35434542	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35527216	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35860642	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35961728	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36112505	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3800023	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3800025	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4490669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55786720	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56030203	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58338781	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59524770	1.00[ASN][1000 genomes]
rs60547490	1.00[ASN][1000 genomes]
rs61340009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459178	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6901944	1.00[GIH][hapmap]
rs6902125	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs71550519	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71564866	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564868	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs720884	1.00[GIH][hapmap]
rs73459728	0.91[ASN][1000 genomes]
rs73459729	1.00[ASN][1000 genomes]
rs73459735	1.00[ASN][1000 genomes]
rs73463711	1.00[ASN][1000 genomes]
rs748996	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7748120	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7748453	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7764446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7771115	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9296855	0.85[TSI][hapmap]
rs9396247	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9475745	1.00[ASN][1000 genomes]
rs9475752	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986245	1.00[CHB][hapmap];1.00[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1599281	BEND6	cis	Artery Tibial	GTEx
rs1599281	RAB23	cis	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56777600-56792600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr6:56777600-56792600	Weak transcription	NH-A	brain
3	chr6:56778400-56792800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:56780600-56792600	Weak transcription	NHLF	lung
5	chr6:56781000-56790600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:56781000-56792600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:56781200-56791600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:56782200-56791600	Weak transcription	Osteobl	bone
9	chr6:56782400-56791200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:56782400-56791600	Weak transcription	NHDF-Ad	bronchial
11	chr6:56782400-56793000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:56782800-56792200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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