Variant report

Variant	rs17685218
Chromosome Location	chr6:56799155-56799156
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10498814	0.82[JPT][hapmap]
rs11962430	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11963350	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1451705	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1451706	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1562908	0.82[JPT][hapmap]
rs1599280	0.80[CEU][hapmap]
rs16888222	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17685235	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1903330	0.80[CEU][hapmap]
rs1903331	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2122958	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2397227	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs35301163	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35818840	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35942895	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58604217	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58721182	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59797084	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61273855	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411410	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411427	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62411428	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62411429	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6459174	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6925107	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs6941401	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs746010	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296855	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9296856	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9370552	0.80[CEU][hapmap]
rs9396250	0.82[JPT][hapmap]
rs9464405	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9464407	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9475744	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17685218	BEND6	cis	Esophagus Muscularis	GTEx
rs17685218	BEND6	cis	lung	GTEx
rs17685218	BEND6	cis	Heart Left Ventricle	GTEx
rs17685218	BEND6	cis	Muscle Skeletal	GTEx

Chromatin state (count:30 , 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	chr6:56793200-56799800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:56793200-56802600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:56793200-56803000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:56793200-56803000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:56793200-56803000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:56793200-56803200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:56796000-56799600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:56796200-56803800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:56796800-56803800	Weak transcription	HSMMtube	muscle
13	chr6:56797400-56799200	Enhancers	Primary hematopoietic stem cells	blood
14	chr6:56797600-56799200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr6:56797600-56801600	Weak transcription	NHLF	lung
16	chr6:56798000-56799800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:56798200-56799800	Weak transcription	NHDF-Ad	bronchial
18	chr6:56798200-56801400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:56798400-56799200	Enhancers	GM12878-XiMat	blood
20	chr6:56798400-56799800	Weak transcription	Osteobl	bone
21	chr6:56798600-56799200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:56798600-56799400	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr6:56798600-56799800	Weak transcription	Brain Anterior Caudate	brain
24	chr6:56798600-56801800	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:56798800-56799800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:56798800-56801200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:56798800-56803400	Weak transcription	K562	blood
28	chr6:56799000-56799200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:56799000-56799200	Flanking Active TSS	Hela-S3	cervix
30	chr6:56799000-56799800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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