Variant report

Variant	rs4245859
Chromosome Location	chr2:142265923-142265924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:142265321..142267918-chr2:142664161..142666622,2	MCF-7	breast:
2	chr2:142261934..142264280-chr2:142265309..142267485,3	MCF-7	breast:
3	chr2:142259654..142261746-chr2:142265611..142267711,3	MCF-7	breast:
4	chr2:142263240..142267352-chr2:142886657..142889435,3	MCF-7	breast:
5	chr2:142248367..142251172-chr2:142262537..142266743,4	MCF-7	breast:
6	chr2:142241833..142244486-chr2:142265674..142268047,2	MCF-7	breast:
7	chr2:142265220..142267079-chr2:142275773..142278354,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168702	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10165979	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10176397	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10176693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10187180	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10200529	0.98[AFR][1000 genomes]
rs10200578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10200582	0.81[AFR][1000 genomes]
rs10200782	1.00[AMR][1000 genomes]
rs10200845	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11887261	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11904458	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12466189	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12472734	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12617980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12618575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12691613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12691614	1.00[AMR][1000 genomes]
rs12691615	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1483138	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1483152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1905292	0.81[AFR][1000 genomes]
rs2128694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2170667	1.00[AMR][1000 genomes]
rs2381110	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381111	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381112	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381113	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381192	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3935992	1.00[AMR][1000 genomes]
rs4008531	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4264515	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4296372	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4359580	1.00[AFR][1000 genomes]
rs4366842	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4396652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4439901	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4441406	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4476294	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4477847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4482418	0.98[AFR][1000 genomes]
rs4482419	0.96[AFR][1000 genomes]
rs4555282	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4954909	1.00[AMR][1000 genomes]
rs4954913	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6429896	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6429897	0.88[AFR][1000 genomes]
rs6429901	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6429902	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6706356	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6706377	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6707441	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6708438	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6710020	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6713043	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6718844	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6737585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6749472	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7557631	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7571511	0.88[AFR][1000 genomes]
rs7572480	1.00[AMR][1000 genomes]
rs7582623	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7585325	1.00[AMR][1000 genomes]
rs7590820	0.89[AFR][1000 genomes]
rs7593866	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7607376	1.00[AMR][1000 genomes]
rs983197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs983198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs983199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs988330	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817518	chr2:141714174-142287302	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv583203	chr2:142055133-142378975	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv875240	chr2:142199421-142347455	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	nsv470491	chr2:142254119-142299923	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
5	nsv834393	chr2:142256714-142431564	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
6	nsv583210	chr2:142259592-142295042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv459629	chr2:142263400-142295042	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv583211	chr2:142263400-142295042	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	nsv583212	chr2:142263979-142309330	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142247800-142266200	Weak transcription	Brain Anterior Caudate	brain
2	chr2:142264000-142266600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:142264000-142268000	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:142264200-142266600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:142265800-142266600	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr2:142265800-142266600	Enhancers	Brain Substantia Nigra	brain
7	chr2:142265800-142266800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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