Variant report

Variant	rs9812989
Chromosome Location	chr3:151172114-151172115
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	chr3:151171469..151173239-chr3:151178441..151180540,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MED12L-3	chr3:151171806-151172346	l_2496_chr3:151171805-151178685_ovary

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13088575	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1491975	0.87[ASN][1000 genomes]
rs2172248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4234322	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435614	0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4679830	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4680440	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680442	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4680443	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6769246	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6774093	0.84[ASN][1000 genomes]
rs6792496	0.82[EUR][1000 genomes]
rs6798252	0.93[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7610769	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7619322	0.94[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7621591	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289838	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9817904	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9824609	0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9825817	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9843590	0.84[JPT][hapmap]
rs9863400	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9871952	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9873499	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9877298	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1000355	chr3:151108859-151243835	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv995048	chr3:151114074-151560019	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv877649	chr3:151147968-151236562	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151161600-151178600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:151168800-151178600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:151169000-151178400	Weak transcription	Aorta	Aorta
4	chr3:151171000-151173800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:151171000-151176200	Weak transcription	Lung	lung
6	chr3:151171200-151173200	Weak transcription	Fetal Lung	lung
7	chr3:151171400-151177200	Weak transcription	Ovary	ovary
8	chr3:151171600-151174600	Weak transcription	Colon Smooth Muscle	Colon

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