Variant report

No.	Distal block	Cell Line	Cell type
1	chr1:224797935..224800597-chr1:224806842..224809051,3	MCF-7	breast:
2	chr1:224802908..224805132-chr1:224806672..224808606,2	MCF-7	breast:
3	chr1:224803029..224804749-chr1:224807138..224809873,2	K562	blood:
4	chr1:224806254..224809054-chr1:224817462..224819155,2	K562	blood:

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction
ENSG00000233384	Chromatin interaction

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10799589	0.83[MEX][hapmap]
rs10916653	0.81[EUR][1000 genomes]
rs12564263	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1353837	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1566386	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1566387	0.85[CEU][hapmap];0.84[MEX][hapmap]
rs1566388	0.84[EUR][1000 genomes]
rs16850250	0.81[CHD][hapmap]
rs1932991	0.80[EUR][1000 genomes]
rs2405317	0.83[EUR][1000 genomes]
rs4654057	0.84[EUR][1000 genomes]
rs4654058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654060	0.84[MEX][hapmap];0.80[EUR][1000 genomes]
rs6658957	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6665204	0.83[EUR][1000 genomes]
rs6690184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697510	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs6699331	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7516323	0.81[EUR][1000 genomes]
rs7529774	0.84[EUR][1000 genomes]
rs7532595	0.83[EUR][1000 genomes]
rs904505	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs883115	C1orf58	cis	parietal	SCAN
rs883115	SNRK	trans	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224803800-224807800	Active TSS	NH-A	brain
2	chr1:224805400-224808000	Flanking Active TSS	Dnd41	blood
3	chr1:224805800-224812200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:224806000-224808800	Bivalent/Poised TSS	Fetal Brain Female	brain
5	chr1:224806000-224811800	Weak transcription	Spleen	Spleen
6	chr1:224806200-224808000	Active TSS	NHLF	lung
7	chr1:224806200-224810400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:224806200-224810400	Weak transcription	Pancreas	Pancrea
9	chr1:224806600-224812800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:224806600-224813600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:224806800-224807600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr1:224807000-224809200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:224807000-224810600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:224807200-224808000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:224807400-224808000	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
16	chr1:224807400-224808800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:224807400-224809800	Weak transcription	HMEC	breast

Quick Search: