Variant report

Variant	rs9868489
Chromosome Location	chr3:160496082-160496083
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	chr3:160489783..160491977-chr3:160495745..160498191,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10513553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487861	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12494732	0.80[JPT][hapmap]
rs12637633	0.82[AMR][1000 genomes]
rs13080397	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs1378654	0.85[ASN][1000 genomes]
rs1378657	0.83[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1378658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1455869	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1598495	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831457	0.80[YRI][hapmap]
rs16831475	0.82[YRI][hapmap]
rs16831478	0.82[YRI][hapmap]
rs1829716	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1839019	0.80[JPT][hapmap]
rs1851378	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1902282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1915929	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2049214	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2049215	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4256178	0.86[CEU][hapmap];0.80[JPT][hapmap];0.83[EUR][1000 genomes]
rs6775743	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6794047	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs718757	0.84[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs722871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618832	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7630250	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7633282	0.82[YRI][hapmap]
rs7648363	0.87[CEU][hapmap]
rs779058	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs972909	0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9809208	0.80[JPT][hapmap]
rs9810290	0.80[JPT][hapmap]
rs9814394	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815499	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9824439	0.80[EUR][1000 genomes]
rs9833075	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9866566	0.84[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160475800-160497200	Weak transcription	Left Ventricle	heart
2	chr3:160476000-160496400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:160477600-160497000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:160477600-160498200	Weak transcription	Stomach Mucosa	stomach
5	chr3:160477800-160497800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:160484400-160496600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:160487200-160502200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:160490200-160498200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:160490400-160496400	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:160490400-160496400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:160490400-160496400	Weak transcription	Fetal Heart	heart
12	chr3:160492400-160498800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:160493200-160496400	Weak transcription	Psoas Muscle	Psoas
14	chr3:160493600-160496200	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:160495000-160502600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:160495200-160497200	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:160495400-160496400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:160495600-160497200	Enhancers	Rectal Smooth Muscle	rectum
19	chr3:160496000-160496400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:160496000-160496600	Enhancers	Skeletal Muscle Female	skeletal muscle

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