Variant report

No.	Distal block	Cell Line	Cell type
1	chr2:99346491..99349928-chr2:99402977..99407960,4	MCF-7	breast:
2	chr2:99402708..99406014-chr2:99411806..99414792,3	MCF-7	breast:
3	chr2:99402180..99404293-chr2:99406318..99408182,2	MCF-7	breast:
4	chr2:99398566..99401288-chr2:99403710..99406748,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071073	Chromatin interaction
ENSG00000201070	Chromatin interaction

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10189330	0.85[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12615689	0.81[TSI][hapmap]
rs12712033	0.90[JPT][hapmap]
rs12712035	0.88[JPT][hapmap]
rs12999225	0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1356424	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1983352	0.90[JPT][hapmap]
rs2276604	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2280256	0.82[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4263159	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6542838	0.90[JPT][hapmap]
rs6711022	0.88[ASN][1000 genomes]
rs6733011	0.80[AMR][1000 genomes]
rs6757099	0.93[ASN][1000 genomes]
rs7579189	0.90[JPT][hapmap]
rs7581128	0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7582382	0.91[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs9308815	0.83[ASN][1000 genomes]
rs981601	0.90[JPT][hapmap]
rs981602	0.90[JPT][hapmap]

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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13389386	ARID5A	cis	parietal	SCAN
rs13389386	FAHD2B	cis	parietal	SCAN
rs13389386	TEKT4	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99385800-99410400	Weak transcription	Right Atrium	heart
2	chr2:99391600-99406600	Weak transcription	Thymus	Thymus
3	chr2:99399400-99404200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:99401800-99412800	Weak transcription	Gastric	stomach
5	chr2:99403200-99404400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
6	chr2:99403400-99412800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:99403800-99404400	Enhancers	Brain Anterior Caudate	brain
8	chr2:99403800-99404600	Enhancers	Fetal Muscle Leg	muscle
9	chr2:99403800-99405000	Enhancers	HepG2	liver

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