Variant report

Variant	rs10406899
Chromosome Location	chr19:42226441-42226442
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	chr19:42217425..42220224-chr19:42223601..42226493,2	MCF-7	breast:
2	chr12:110150287..110151979-chr19:42225644..42228093,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10403308	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10408799	0.84[ASN][1000 genomes]
rs10411488	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10412553	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10414063	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10415317	0.84[ASN][1000 genomes]
rs10415946	0.84[ASN][1000 genomes]
rs10417322	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10421687	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10425443	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10853754	0.85[ASN][1000 genomes]
rs11083637	0.97[ASN][1000 genomes]
rs1115885	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11667651	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11672324	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11673394	0.85[ASN][1000 genomes]
rs11878239	0.82[ASN][1000 genomes]
rs11878262	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11881921	0.88[ASN][1000 genomes]
rs12971712	0.83[ASN][1000 genomes]
rs12973096	0.84[ASN][1000 genomes]
rs12985771	0.91[ASN][1000 genomes]
rs1593086	0.99[ASN][1000 genomes]
rs2002926	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2113133	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2113134	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2161625	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764577	0.84[ASN][1000 genomes]
rs3764579	0.84[ASN][1000 genomes]
rs3829668	0.84[ASN][1000 genomes]
rs3928916	0.81[ASN][1000 genomes]
rs4239514	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4802127	0.87[ASN][1000 genomes]
rs4802128	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4802129	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4802130	0.83[ASN][1000 genomes]
rs4803503	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803505	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803506	0.86[ASN][1000 genomes]
rs55997514	0.90[ASN][1000 genomes]
rs7247317	0.91[ASN][1000 genomes]
rs7252828	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7255070	0.84[ASN][1000 genomes]
rs748249	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8106723	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs987066	0.84[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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061309	chr19:42187716-42228445	Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv482220	chr19:42212530-42234436	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv3425986	chr19:42212540-42259719	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv579615	chr19:42221434-42310388	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr19:42216600-42228200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr19:42217800-42230200	Strong transcription	Rectal Mucosa Donor 31	rectum
3	chr19:42217800-42231200	Weak transcription	Fetal Intestine Small	intestine
4	chr19:42222000-42227800	Weak transcription	Esophagus	oesophagus
5	chr19:42223000-42230600	Weak transcription	Stomach Mucosa	stomach
6	chr19:42225800-42230400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr19:42226200-42230000	Weak transcription	Colonic Mucosa	Colon
8	chr19:42226400-42230000	Weak transcription	Rectal Mucosa Donor 29	rectum

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