Variant report

Variant	rs6490422
Chromosome Location	chr13:30268094-30268095
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	chr13:30166226..30170537-chr13:30267927..30269941,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139514	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1010154	0.94[ASN][1000 genomes]
rs12854213	0.94[ASN][1000 genomes]
rs12870250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12870927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1467601	0.80[ASN][1000 genomes]
rs1590696	0.96[ASN][1000 genomes]
rs1752040	0.96[ASN][1000 genomes]
rs17625129	0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2078408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[ASN][1000 genomes]
rs3858738	0.90[CEU][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4769767	0.95[ASN][1000 genomes]
rs4769768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4769769	0.93[ASN][1000 genomes]
rs6490421	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6490423	0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6490424	0.99[ASN][1000 genomes]
rs7317991	0.99[ASN][1000 genomes]
rs7318002	0.99[ASN][1000 genomes]
rs7333892	0.99[ASN][1000 genomes]
rs7337296	0.90[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7991022	0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs9508530	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9508532	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9508533	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9508534	0.98[ASN][1000 genomes]
rs9508535	0.98[ASN][1000 genomes]
rs9508536	0.95[ASN][1000 genomes]
rs9508537	0.96[ASN][1000 genomes]
rs9508538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9508539	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs9508540	0.84[ASN][1000 genomes]
rs9508541	0.96[ASN][1000 genomes]
rs9550489	0.95[ASN][1000 genomes]
rs9551721	0.81[ASN][1000 genomes]
rs9551722	0.94[ASN][1000 genomes]
rs9578132	0.89[CHB][hapmap]
rs9579471	0.93[ASN][1000 genomes]
rs9634355	0.95[ASN][1000 genomes]
rs997896	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899961	chr13:30226924-30407273	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30266200-30268800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr13:30266400-30268400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:30267000-30268400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:30267000-30268400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr13:30267400-30268200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr13:30267400-30268200	Flanking Active TSS	NHEK	skin
7	chr13:30267400-30268400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:30267400-30268400	Enhancers	HMEC	breast
9	chr13:30268000-30269000	Weak transcription	Esophagus	oesophagus

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