Variant report

Variant	rs1425533
Chromosome Location	chr4:143421175-143421176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:143406582..143409502-chr4:143418900..143421549,4	MCF-7	breast:
2	chr4:143420911..143422875-chr4:143427108..143429305,2	MCF-7	breast:
3	chr4:143392241..143398966-chr4:143412985..143424496,30	MCF-7	breast:
4	chr4:143418608..143422972-chr4:143431546..143435258,5	MCF-7	breast:
5	chr4:143388381..143398737-chr4:143415738..143428678,26	MCF-7	breast:
6	chr4:143420095..143422300-chr4:143536470..143540708,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10011782	1.00[CEU][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs12108640	0.92[EUR][1000 genomes]
rs12642500	0.83[AFR][1000 genomes]
rs1391099	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs1425531	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1425536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425537	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1489581	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs17016163	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs17016175	0.92[CEU][hapmap];0.86[TSI][hapmap]
rs17016248	0.86[CHD][hapmap]
rs17016304	0.84[CHD][hapmap]
rs17016306	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1817970	0.84[CEU][hapmap]
rs1834391	0.94[EUR][1000 genomes]
rs2113996	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113997	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2322795	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2874841	0.91[EUR][1000 genomes]
rs2874865	0.94[EUR][1000 genomes]
rs28822497	0.90[EUR][1000 genomes]
rs3844178	0.93[EUR][1000 genomes]
rs3913163	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs4975308	0.92[EUR][1000 genomes]
rs60924405	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713071	0.93[EUR][1000 genomes]
rs7668133	0.82[JPT][hapmap]
rs7672965	0.92[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap]
rs976564	0.94[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr4:143419200-143421200	Weak transcription	Fetal Heart	heart
2	chr4:143420400-143421800	Weak transcription	Stomach Mucosa	stomach
3	chr4:143421000-143421600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:143421000-143421600	Enhancers	Ovary	ovary
5	chr4:143421000-143422400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:143421000-143422600	Enhancers	Fetal Intestine Large	intestine

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