Variant report

Variant	rs12642500
Chromosome Location	chr4:143422018-143422019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000109452	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10012476	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10015184	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1013397	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12643136	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12644565	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12646243	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649139	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364917	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1364918	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1364919	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1364920	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1364926	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1425533	0.83[AFR][1000 genomes]
rs1425534	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425535	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425536	0.83[AFR][1000 genomes]
rs1425538	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17016170	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17016207	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17016248	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17016284	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17016304	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2042644	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2113997	0.90[ASN][1000 genomes]
rs2162108	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2322705	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2322706	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2322796	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28510314	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28823374	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28850298	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28861843	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34900920	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4345256	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57724540	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59784151	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60004938	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6823362	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7668133	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7672965	0.80[ASN][1000 genomes]
rs7699408	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9308152	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9986090	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9998089	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][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:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143421000-143422400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:143421000-143422600	Enhancers	Fetal Intestine Large	intestine
3	chr4:143421200-143422600	Enhancers	Fetal Heart	heart
4	chr4:143421400-143422600	Enhancers	Fetal Intestine Small	intestine
5	chr4:143421800-143422600	Enhancers	Stomach Mucosa	stomach

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