Variant report

Variant	rs6594590
Chromosome Location	chr5:111676755-111676756
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:111676724..111678269-chr5:111678976..111680650,2	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10039730	1.00[JPT][hapmap]
rs10044406	1.00[JPT][hapmap]
rs10051512	1.00[JPT][hapmap]
rs10060962	1.00[JPT][hapmap]
rs10061025	1.00[JPT][hapmap]
rs10061207	1.00[JPT][hapmap]
rs10062045	1.00[JPT][hapmap]
rs10068969	1.00[JPT][hapmap]
rs10068974	1.00[JPT][hapmap]
rs10069608	1.00[JPT][hapmap]
rs10069773	1.00[JPT][hapmap]
rs10071058	1.00[JPT][hapmap]
rs10071862	1.00[JPT][hapmap]
rs10071986	1.00[JPT][hapmap]
rs10072705	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10077774	1.00[JPT][hapmap]
rs10079307	1.00[JPT][hapmap]
rs10478081	1.00[JPT][hapmap]
rs10478082	1.00[JPT][hapmap]
rs10478083	1.00[JPT][hapmap]
rs10478084	1.00[JPT][hapmap]
rs10515444	1.00[JPT][hapmap]
rs12187850	1.00[JPT][hapmap]
rs13354202	1.00[JPT][hapmap]
rs13354699	1.00[JPT][hapmap]
rs1524423	1.00[JPT][hapmap]
rs1554624	1.00[JPT][hapmap]
rs17134335	0.84[ASN][1000 genomes]
rs17134357	0.84[ASN][1000 genomes]
rs17134381	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17134382	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17134384	0.92[ASN][1000 genomes]
rs17134423	1.00[JPT][hapmap]
rs17134426	1.00[JPT][hapmap]
rs17134429	1.00[JPT][hapmap]
rs17134454	1.00[JPT][hapmap]
rs17134478	1.00[JPT][hapmap]
rs17134503	1.00[JPT][hapmap]
rs17134505	1.00[JPT][hapmap]
rs2416285	1.00[JPT][hapmap]
rs388383	1.00[JPT][hapmap]
rs3985058	1.00[JPT][hapmap]
rs448714	1.00[JPT][hapmap]
rs56018262	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57004301	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57211830	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57778181	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60021992	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60193147	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60730910	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60806157	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60836718	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6594594	1.00[JPT][hapmap]
rs6594596	1.00[JPT][hapmap]
rs6860402	1.00[JPT][hapmap]
rs6863425	0.92[ASN][1000 genomes]
rs6863610	1.00[JPT][hapmap]
rs6865127	1.00[JPT][hapmap]
rs6865715	1.00[JPT][hapmap]
rs6867914	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6875349	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6878092	1.00[JPT][hapmap]
rs6878158	1.00[JPT][hapmap]
rs6879906	1.00[JPT][hapmap]
rs6883585	1.00[JPT][hapmap]
rs6883800	1.00[JPT][hapmap]
rs6884339	1.00[JPT][hapmap]
rs6890476	1.00[JPT][hapmap]
rs6891512	1.00[JPT][hapmap]
rs6893840	1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6894365	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs721054	1.00[JPT][hapmap]
rs721055	1.00[JPT][hapmap]
rs7702999	1.00[JPT][hapmap]
rs7703875	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7706551	1.00[JPT][hapmap]
rs7706737	1.00[JPT][hapmap]
rs7707028	1.00[JPT][hapmap]
rs7709879	1.00[JPT][hapmap]
rs7709963	1.00[JPT][hapmap]
rs7710041	1.00[JPT][hapmap]
rs7710507	1.00[JPT][hapmap]
rs7714258	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7716246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7716394	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7720272	0.84[ASN][1000 genomes]
rs7723364	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7725728	1.00[JPT][hapmap]
rs7730739	1.00[JPT][hapmap]
rs7733415	1.00[JPT][hapmap]
rs7736305	1.00[JPT][hapmap]
rs7737622	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs821738	1.00[CHB][hapmap]
rs821739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs821746	1.00[JPT][hapmap]
rs821750	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9326853	1.00[JPT][hapmap]
rs985873	1.00[JPT][hapmap]
rs986797	1.00[JPT][hapmap]
rs9885137	1.00[JPT][hapmap]
rs9885182	1.00[JPT][hapmap]
rs9885390	1.00[JPT][hapmap]
rs999243	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh 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	26 gene(s)	inside rSNPs	diseases
3	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1021530	chr5:111626266-111683317	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1028181	chr5:111628901-111683317	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv882714	chr5:111655382-111807579	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv462386	chr5:111667572-111699317	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv599372	chr5:111667572-111699317	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111637400-111684600	Weak transcription	Aorta	Aorta
2	chr5:111669400-111678000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:111669600-111677800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr5:111669800-111683600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:111673600-111676800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:111674200-111678200	Weak transcription	Pancreas	Pancrea
7	chr5:111674400-111678000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr5:111674800-111678000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:111675000-111677000	Enhancers	Hela-S3	cervix
10	chr5:111675000-111677800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:111675000-111677800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:111675000-111677800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr5:111675000-111678000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:111675000-111678000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:111675000-111678000	Enhancers	Fetal Heart	heart
16	chr5:111675000-111678000	Weak transcription	Gastric	stomach
17	chr5:111675000-111678200	Weak transcription	Adipose Nuclei	Adipose
18	chr5:111675000-111678200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:111675000-111678400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:111675000-111678600	Weak transcription	Brain Anterior Caudate	brain
21	chr5:111675000-111682800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr5:111675600-111687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:111675800-111678000	Weak transcription	Brain Hippocampus Middle	brain
24	chr5:111676000-111678000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:111676200-111676800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:111676200-111678000	Weak transcription	Right Ventricle	heart
27	chr5:111676200-111678200	Weak transcription	Left Ventricle	heart
28	chr5:111676200-111678200	Weak transcription	Right Atrium	heart
29	chr5:111676200-111689000	Weak transcription	Lung	lung
30	chr5:111676400-111678000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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