Variant report

Variant	rs12376539
Chromosome Location	chr9:94590770-94590771
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	chr9:94588743..94592515-chr9:94595352..94598489,3	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10820906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10820907	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10992123	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs10992124	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs10992128	0.88[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs10992129	0.85[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs10992130	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs10992131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992132	0.86[CEU][hapmap]
rs10992134	0.86[CEU][hapmap]
rs10992135	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10992137	0.86[CEU][hapmap]
rs10992139	0.87[CEU][hapmap]
rs10992142	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10992143	0.83[CEU][hapmap]
rs10992144	0.83[CEU][hapmap]
rs10992145	0.83[CEU][hapmap]
rs11791450	0.95[CEU][hapmap]
rs12376231	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12378938	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12551140	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12552292	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs12552858	0.86[CEU][hapmap]
rs12684524	0.82[CEU][hapmap]
rs1528363	0.83[CEU][hapmap]
rs1528364	0.83[CEU][hapmap]
rs1534531	0.83[EUR][1000 genomes]
rs16907887	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs1881385	0.82[CEU][hapmap]
rs1881387	0.82[CEU][hapmap]
rs1881392	0.86[CEU][hapmap]
rs1997286	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2312732	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2312734	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312735	0.82[CEU][hapmap]
rs2841691	0.82[EUR][1000 genomes]
rs4322068	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4639579	0.87[CEU][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs4743857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4744107	0.83[CEU][hapmap]
rs55663665	0.82[EUR][1000 genomes]
rs62564595	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62564597	0.80[EUR][1000 genomes]
rs62564598	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479374	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6479375	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479376	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs7019210	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7029950	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7031562	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7033819	0.83[CEU][hapmap]
rs7039406	0.87[CEU][hapmap]
rs7045333	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7048756	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72746206	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7850118	0.84[CEU][hapmap]
rs7855417	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs7856144	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7859331	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7863061	0.87[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs7867707	0.87[CEU][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs7870902	0.83[EUR][1000 genomes]
rs7874148	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking 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	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv518372	chr9:94558126-94605908	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv6614	chr9:94571349-94610085	ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94584000-94595800	Weak transcription	Gastric	stomach
2	chr9:94588000-94595800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr9:94588000-94596000	Weak transcription	Fetal Intestine Small	intestine
4	chr9:94588200-94594000	Weak transcription	Fetal Stomach	stomach
5	chr9:94588200-94595400	Weak transcription	Ovary	ovary
6	chr9:94588200-94595800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:94588200-94595800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:94588600-94594600	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:94588600-94595400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:94590200-94592800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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