Variant report

Variant	rs17428273
Chromosome Location	chr6:39301627-39301628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10484827	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11751122	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11751171	1.00[AFR][1000 genomes]
rs11751584	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11751610	0.89[ASN][1000 genomes]
rs11753201	0.83[AMR][1000 genomes]
rs11753468	1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11754376	0.91[AMR][1000 genomes]
rs11756084	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11756686	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11756848	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11757747	1.00[AFR][1000 genomes]
rs11758036	1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs11758206	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11758639	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11758789	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11759440	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16891940	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16892032	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17351024	1.00[JPT][hapmap]
rs17429762	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs34369766	0.89[ASN][1000 genomes]
rs35376357	0.89[ASN][1000 genomes]
rs4312982	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56370893	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56979582	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59352627	0.89[ASN][1000 genomes]
rs60227351	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72858442	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72858444	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72858446	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72858448	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72858451	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72858468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72858469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72858477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72858494	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73731792	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7742057	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9296295	1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv533806	chr6:39270073-39397337	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39285600-39307800	Weak transcription	Esophagus	oesophagus
2	chr6:39297000-39303600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:39298400-39303400	Weak transcription	Aorta	Aorta
4	chr6:39298600-39303200	Weak transcription	Spleen	Spleen
5	chr6:39298600-39304200	Weak transcription	Brain Hippocampus Middle	brain
6	chr6:39298800-39303600	Weak transcription	GM12878-XiMat	blood
7	chr6:39298800-39305800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:39298800-39306400	Weak transcription	Gastric	stomach
9	chr6:39298800-39307800	Weak transcription	Brain Anterior Caudate	brain
10	chr6:39298800-39310600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:39299000-39302600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:39299000-39302600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:39299000-39303600	Weak transcription	Primary B cells from cord blood	blood
14	chr6:39300200-39303600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr6:39300200-39303600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:39300400-39304800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr6:39300600-39302600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:39300600-39307400	Weak transcription	Brain Substantia Nigra	brain
19	chr6:39301000-39302400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:39301000-39304600	Enhancers	Adipose Nuclei	Adipose
21	chr6:39301200-39302000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:39301200-39302000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:39301200-39302000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:39301200-39302000	Enhancers	Fetal Stomach	stomach
25	chr6:39301400-39301800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:39301400-39301800	Weak transcription	Right Atrium	heart
27	chr6:39301600-39307200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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