Variant report

Variant	rs1598495
Chromosome Location	chr3:160497731-160497732
allele	A/G
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: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10513553	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486979	0.82[EUR][1000 genomes]
rs12487861	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs12494732	0.80[JPT][hapmap]
rs13068380	0.89[EUR][1000 genomes]
rs1378654	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1378657	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1378658	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1403048	0.82[EUR][1000 genomes]
rs1455869	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1829716	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1839019	0.80[JPT][hapmap]
rs1851378	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1902282	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1915929	0.88[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2049214	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2049215	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2886905	0.83[EUR][1000 genomes]
rs4256178	0.80[JPT][hapmap]
rs59542611	0.90[EUR][1000 genomes]
rs6775743	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs6781371	0.81[EUR][1000 genomes]
rs6794047	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6805905	0.83[EUR][1000 genomes]
rs718757	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.90[EUR][1000 genomes]
rs722871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7630250	0.91[ASN][1000 genomes]
rs7634342	0.83[EUR][1000 genomes]
rs7640348	0.81[EUR][1000 genomes]
rs7642371	0.83[EUR][1000 genomes]
rs7643513	0.82[EUR][1000 genomes]
rs779058	0.91[ASN][1000 genomes]
rs972909	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9809208	0.80[JPT][hapmap]
rs9810290	0.80[JPT][hapmap]
rs9814394	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815499	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9833075	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9866566	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9868489	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]

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	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
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160477600-160498200	Weak transcription	Stomach Mucosa	stomach
2	chr3:160477800-160497800	Weak transcription	Brain Angular Gyrus	brain
3	chr3:160487200-160502200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:160490200-160498200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:160492400-160498800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:160495000-160502600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:160496200-160498600	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:160496200-160501000	Enhancers	Colon Smooth Muscle	Colon
9	chr3:160496400-160498400	Weak transcription	Fetal Brain Female	brain
10	chr3:160496400-160499400	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr3:160496400-160499600	Enhancers	Psoas Muscle	Psoas
12	chr3:160496400-160499600	Enhancers	Stomach Smooth Muscle	stomach
13	chr3:160496600-160498200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:160496600-160499400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:160496600-160503400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:160496800-160498000	Weak transcription	Fetal Heart	heart
17	chr3:160496800-160501600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:160497000-160498200	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:160497000-160498600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:160497000-160499600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:160497200-160498000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:160497200-160498000	Enhancers	Left Ventricle	heart
23	chr3:160497200-160498200	Weak transcription	Primary T cells from cord blood	blood
24	chr3:160497200-160498200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:160497200-160498200	Weak transcription	Brain Substantia Nigra	brain
26	chr3:160497200-160498200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:160497200-160498200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr3:160497200-160498400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:160497200-160499600	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr3:160497200-160502000	Weak transcription	H1 Cell Line	embryonic stem cell

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