Variant report

Variant	rs10249
Chromosome Location	chr9:71911684-71911685
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:71910612..71916795-chr9:71938109..71942701,9	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-APBA1-3	chr9:71911599-71911783	XLOC_007724
2	lnc-APBA1-3	chr9:71911597-71911783	NR_047671
3	lnc-APBA1-3	chr9:71911594-71911783	XLOC_007724

Variant related genes	Relation type
ENSG00000135063	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10780251	0.81[AMR][1000 genomes]
rs10780256	0.83[AMR][1000 genomes]
rs10780257	0.83[AMR][1000 genomes]
rs10867330	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11137955	0.82[EUR][1000 genomes]
rs1416737	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890635	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1890637	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1890638	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2095347	0.92[CEU][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309415	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2309416	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2309417	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2309429	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2309430	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28800827	0.85[ASN][1000 genomes]
rs4308798	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4744872	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7027248	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7030339	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7030477	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv831610	chr9:71846941-72016835	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71909400-71912000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:71910400-71912200	Enhancers	Right Ventricle	heart
3	chr9:71910400-71913200	Enhancers	Left Ventricle	heart
4	chr9:71910800-71913200	Enhancers	Fetal Lung	lung
5	chr9:71911000-71911800	Bivalent Enhancer	HSMMtube	muscle
6	chr9:71911000-71912400	Enhancers	Stomach Smooth Muscle	stomach
7	chr9:71911000-71913000	Enhancers	Ovary	ovary
8	chr9:71911000-71913600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:71911200-71911800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:71911200-71912200	Weak transcription	Lung	lung
11	chr9:71911200-71912600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr9:71911400-71911800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr9:71911400-71911800	Enhancers	Fetal Heart	heart
14	chr9:71911400-71911800	Weak transcription	Fetal Muscle Leg	muscle
15	chr9:71911400-71912400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr9:71911600-71912400	Enhancers	Skeletal Muscle Female	skeletal muscle

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