Variant report

Variant	rs10403308
Chromosome Location	chr19:42229656-42229657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42212393..42215369-chr19:42228630..42231266,2	MCF-7	breast:
2	chr19:42229256..42231209-chr19:42253905..42256150,2	K562	blood:
3	chr19:42217628..42220315-chr19:42227201..42229825,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105388	Chromatin interaction
ENSG00000267881	Chromatin interaction
ENSG00000086548	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10406899	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10408799	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10411488	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10412553	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414063	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10415317	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10415946	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10417322	0.89[ASN][1000 genomes]
rs10421687	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10425443	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10853754	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083637	0.87[ASN][1000 genomes]
rs1115885	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11667651	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11672324	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11673394	0.88[CHB][hapmap]
rs11878239	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11878262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881921	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12971712	0.88[CHB][hapmap]
rs12973096	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12985771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1593086	0.89[ASN][1000 genomes]
rs2002926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113133	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2113134	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2161625	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3764577	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3764579	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3829668	0.94[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3928916	0.88[CHB][hapmap]
rs4239514	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802128	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802129	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802130	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803503	0.90[ASN][1000 genomes]
rs4803505	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55997514	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71334991	0.85[AMR][1000 genomes]
rs7247317	0.82[ASN][1000 genomes]
rs7252828	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255070	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs748249	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8105784	0.85[AMR][1000 genomes]
rs8106723	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs987066	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[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	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	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
3	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
4	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:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42217800-42230200	Strong transcription	Rectal Mucosa Donor 31	rectum
2	chr19:42217800-42231200	Weak transcription	Fetal Intestine Small	intestine
3	chr19:42223000-42230600	Weak transcription	Stomach Mucosa	stomach
4	chr19:42225800-42230400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr19:42226200-42230000	Weak transcription	Colonic Mucosa	Colon
6	chr19:42226400-42230000	Weak transcription	Rectal Mucosa Donor 29	rectum

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