Variant report

Variant	rs1576611
Chromosome Location	chr13:38947248-38947249
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:38923241..38925900-chr13:38946340..38949227,2	MCF-7	breast:
2	chr13:38922928..38925476-chr13:38947083..38949963,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UFM1-9	chr13:38946993-38948072	NONHSAT033274

Variant related genes	Relation type
ENSG00000120686	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11693	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330958	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330960	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330964	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330965	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360385	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553300	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576610	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980984	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019520	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150468	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150469	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231323	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231328	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231330	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231332	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455412	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481876	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481877	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481879	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481880	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485783	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485785	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485786	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485789	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496456	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496473	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496475	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496476	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943581	0.83[ASN][1000 genomes]
rs4943583	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943584	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943585	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943586	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563608	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563609	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326028	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326913	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332974	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7335723	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338958	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285122	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532209	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532217	0.93[AFR][1000 genomes]
rs9532218	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548318	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548320	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603368	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986773	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949406	chr13:38561474-39033484	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv900006	chr13:38924871-38970825	Genic enhancers ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1851668	chr13:38928976-38948851	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38942200-38951000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:38944200-38949600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr13:38946800-38947400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:38947000-38947400	Enhancers	Ovary	ovary
5	chr13:38947000-38947600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr13:38947200-38947600	Flanking Active TSS	Hela-S3	cervix
7	chr13:38947200-38948000	Enhancers	HepG2	liver

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