Variant report

Variant	rs878460
Chromosome Location	chr3:112839515-112839516
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	chr3:112838001..112839541-chr3:112853891..112856823,2	MCF-7	breast:
2	chr3:112831326..112834195-chr3:112837438..112839554,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10934216	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934217	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486277	0.84[AMR][1000 genomes]
rs1632500	0.83[AFR][1000 genomes]
rs1795161	0.84[AMR][1000 genomes]
rs1795174	0.83[AFR][1000 genomes]
rs1797608	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1797616	0.85[AFR][1000 genomes]
rs1797617	0.86[AFR][1000 genomes]
rs1797621	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1797622	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1881943	0.85[AMR][1000 genomes]
rs1881947	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2004990	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2017828	0.85[ASN][1000 genomes]
rs2045687	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2045688	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2045690	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2045691	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2613919	0.98[ASN][1000 genomes]
rs2613920	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2613921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2613922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613957	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2700202	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700203	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2700204	0.98[ASN][1000 genomes]
rs2700205	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2700206	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2700209	0.83[AFR][1000 genomes]
rs2700210	0.83[AFR][1000 genomes]
rs2700214	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2700215	0.83[AFR][1000 genomes]
rs2700216	0.83[AFR][1000 genomes]
rs2926811	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2951458	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2951459	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2951460	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2951461	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2951462	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2951463	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2951464	0.83[AFR][1000 genomes]
rs3101349	0.86[AFR][1000 genomes]
rs3852010	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3852011	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4383482	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4387939	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62262831	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6438130	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807101	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7632483	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650532	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818149	0.83[ASN][1000 genomes]
rs9829983	0.82[AMR][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv877344	chr3:112789865-112854339	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv877345	chr3:112826253-112848851	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112835800-112840600	Enhancers	Fetal Stomach	stomach
2	chr3:112837000-112842200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:112837600-112842800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:112837600-112842800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:112837600-112842800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:112837800-112840000	Weak transcription	Fetal Lung	lung
7	chr3:112839000-112840400	Enhancers	Colon Smooth Muscle	Colon
8	chr3:112839200-112840600	Enhancers	Rectal Smooth Muscle	rectum
9	chr3:112839400-112839600	Enhancers	Fetal Muscle Trunk	muscle

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