Variant report

Variant	rs17752459
Chromosome Location	chr6:56798755-56798756
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs13215865	0.81[EUR][1000 genomes]
rs13220510	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1451707	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1451708	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1460561	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1599280	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1599281	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17450853	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17685143	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17685185	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17752412	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17752435	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1903330	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34232358	0.81[EUR][1000 genomes]
rs34259328	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34714091	0.81[EUR][1000 genomes]
rs34733863	0.81[EUR][1000 genomes]
rs34752771	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34812189	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35202312	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35434542	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35527216	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35860642	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35961728	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36112505	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4490669	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55786720	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56030203	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58338781	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61340009	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71550519	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564866	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71564868	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs748996	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17752459	BEND6	cis	Artery Tibial	GTEx

Chromatin state (count:31 , 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	chr6:56793200-56799000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr6:56793200-56799800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:56793200-56802600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:56793200-56803000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:56793200-56803000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:56793200-56803000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:56793200-56803200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:56796000-56799600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:56796200-56803800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:56796800-56803800	Weak transcription	HSMMtube	muscle
14	chr6:56797000-56798800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:56797400-56798800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr6:56797400-56799200	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:56797600-56799200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr6:56797600-56801600	Weak transcription	NHLF	lung
19	chr6:56797800-56798800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:56798000-56799800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:56798200-56798800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr6:56798200-56799800	Weak transcription	NHDF-Ad	bronchial
23	chr6:56798200-56801400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:56798400-56799200	Enhancers	GM12878-XiMat	blood
25	chr6:56798400-56799800	Weak transcription	Osteobl	bone
26	chr6:56798600-56798800	Flanking Active TSS	Hela-S3	cervix
27	chr6:56798600-56798800	Enhancers	K562	blood
28	chr6:56798600-56799200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:56798600-56799400	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:56798600-56799800	Weak transcription	Brain Anterior Caudate	brain
31	chr6:56798600-56801800	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links