Variant report

Variant	rs13180409
Chromosome Location	chr5:90358300-90358301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90343505..90346725-chr5:90355686..90358630,4	MCF-7	breast:
2	chr5:90356230..90358804-chr5:90678069..90680261,3	K562	blood:
3	chr5:90358015..90360678-chr5:90675841..90680032,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

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

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

rs_ID	r²[population]
rs10942624	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12186662	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13179479	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1819073	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1819074	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1828177	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1828178	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1848486	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1848487	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1852734	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858070	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap]
rs2048217	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2367186	0.92[ASN][1000 genomes]
rs2367274	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2463775	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2662278	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2662279	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2662280	0.91[CEU][hapmap];0.90[GIH][hapmap];0.82[EUR][1000 genomes]
rs2662281	0.88[ASN][1000 genomes]
rs2662282	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2662283	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2662284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2697543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2697544	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2697546	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28875340	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4254936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4454077	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6452930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6452934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6452935	0.85[AMR][1000 genomes]
rs6865615	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap]
rs6882081	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689544	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7706034	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7719311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7723511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7733230	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs937920	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs998788	0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[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	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 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	chr5:90341200-90376600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr5:90344800-90368000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:90349600-90358400	Weak transcription	Fetal Kidney	kidney
4	chr5:90352400-90367000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:90354200-90359600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:90354600-90359000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:90354800-90368200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:90355200-90358400	Weak transcription	Colon Smooth Muscle	Colon
9	chr5:90357200-90358600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr5:90357200-90359800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:90357400-90358400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr5:90357400-90359400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:90357600-90358400	Flanking Active TSS	GM12878-XiMat	blood
14	chr5:90357600-90358800	Enhancers	Stomach Mucosa	stomach
15	chr5:90357800-90358800	Enhancers	Fetal Lung	lung
16	chr5:90357800-90359200	Enhancers	Primary hematopoietic stem cells	blood
17	chr5:90357800-90359200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr5:90358000-90358400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:90358000-90358600	Enhancers	Brain Anterior Caudate	brain
20	chr5:90358000-90358600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr5:90358000-90359000	Enhancers	Fetal Muscle Leg	muscle
22	chr5:90358000-90359800	Enhancers	Ovary	ovary
23	chr5:90358200-90358400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:90358200-90358400	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr5:90358200-90358600	Enhancers	Aorta	Aorta
26	chr5:90358200-90358600	Enhancers	Gastric	stomach
27	chr5:90358200-90359200	Enhancers	Sigmoid Colon	Sigmoid Colon

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