Variant report

Variant	rs12899740
Chromosome Location	chr15:51599361-51599362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51590787..51593920-chr15:51596924..51599440,3	K562	blood:
2	chr15:51599001..51601083-chr15:51656422..51658497,2	MCF-7	breast:
3	chr15:51598697..51600244-chr15:51613341..51616077,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10519302	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12439794	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12594203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12594287	0.82[CEU][hapmap]
rs12595570	0.81[EUR][1000 genomes]
rs12900137	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964201	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs16964211	0.82[CEU][hapmap]
rs16964220	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs16964221	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs16964254	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16964258	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17647707	1.00[CEU][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs17647719	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17703982	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1865803	0.82[CEU][hapmap]
rs1902582	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1902586	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs28538925	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28559787	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28566535	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28719042	0.81[EUR][1000 genomes]
rs28723025	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28757111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28757122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28757156	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs28757157	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs28757159	0.88[CHB][hapmap]
rs2899473	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs3764221	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4614671	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4775934	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs59944627	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176453	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181886	1.00[CEU][hapmap]
rs726547	0.82[CEU][hapmap]
rs7342683	0.83[EUR][1000 genomes]
rs74013190	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8030862	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031463	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9302160	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9806371	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs999480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51591400-51602800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:51591800-51604600	Weak transcription	Gastric	stomach
3	chr15:51592200-51615000	Weak transcription	Spleen	Spleen
4	chr15:51594600-51602200	Weak transcription	HepG2	liver
5	chr15:51596600-51600000	Weak transcription	Right Ventricle	heart
6	chr15:51596600-51602000	Weak transcription	Fetal Lung	lung
7	chr15:51599000-51599800	Enhancers	Adipose Nuclei	Adipose
8	chr15:51599200-51599400	Enhancers	Left Ventricle	heart
9	chr15:51599200-51600400	Enhancers	Right Atrium	heart
10	chr15:51599200-51600600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:51599200-51600800	Strong transcription	Placenta	Placenta

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