Variant report

Variant	rs4439901
Chromosome Location	chr2:142244389-142244390
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:142241833..142244486-chr2:142265674..142268047,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10165979	1.00[AMR][1000 genomes]
rs10167487	0.88[YRI][hapmap]
rs10176397	1.00[AMR][1000 genomes]
rs10176693	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10187180	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10191434	0.86[YRI][hapmap]
rs10200529	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10200578	0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10200782	1.00[AMR][1000 genomes]
rs10200845	1.00[AMR][1000 genomes]
rs1038346	0.88[YRI][hapmap]
rs11887261	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11904458	1.00[AMR][1000 genomes]
rs12466189	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12472734	1.00[AMR][1000 genomes]
rs12617980	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12618575	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12691613	0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12691614	1.00[AMR][1000 genomes]
rs12691615	1.00[AMR][1000 genomes]
rs1483138	1.00[AMR][1000 genomes]
rs1483152	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2128694	1.00[AMR][1000 genomes]
rs2170667	1.00[AMR][1000 genomes]
rs2381110	1.00[AMR][1000 genomes]
rs2381111	1.00[AMR][1000 genomes]
rs2381112	1.00[AMR][1000 genomes]
rs2381113	1.00[AMR][1000 genomes]
rs2381192	1.00[AMR][1000 genomes]
rs3856360	0.88[YRI][hapmap]
rs3935992	1.00[AMR][1000 genomes]
rs4008531	1.00[AMR][1000 genomes]
rs4245859	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4264515	1.00[AMR][1000 genomes]
rs4296372	0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4359580	0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs4366842	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4396652	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4441406	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4446017	1.00[YRI][hapmap]
rs4476294	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4477847	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4482418	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs4555282	1.00[AMR][1000 genomes]
rs4954909	1.00[AMR][1000 genomes]
rs4954913	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5001568	1.00[YRI][hapmap]
rs6429896	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6429897	0.94[AFR][1000 genomes]
rs6429901	1.00[AMR][1000 genomes]
rs6429902	1.00[AMR][1000 genomes]
rs6706356	1.00[AMR][1000 genomes]
rs6706377	1.00[AMR][1000 genomes]
rs6707422	0.88[YRI][hapmap]
rs6707441	0.88[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6708438	1.00[AMR][1000 genomes]
rs6710020	1.00[AMR][1000 genomes]
rs6713043	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6718844	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6730292	0.82[YRI][hapmap]
rs6737585	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6749472	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7557631	1.00[AMR][1000 genomes]
rs7571511	0.94[AFR][1000 genomes]
rs7572480	1.00[AMR][1000 genomes]
rs7582623	1.00[AMR][1000 genomes]
rs7585325	1.00[AMR][1000 genomes]
rs7590820	0.88[YRI][hapmap]
rs7593866	1.00[AMR][1000 genomes]
rs7607376	1.00[AMR][1000 genomes]
rs983197	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs983198	0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs983199	0.83[AFR][1000 genomes];1.00[AMR][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	esv2759095	chr2:142071391-142245947	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv875234	chr2:142156180-142254119	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv2756949	chr2:142196123-142245947	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	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
7	nsv875243	chr2:142219033-142259592	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv459607	chr2:142226768-142263400	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv583207	chr2:142226768-142263400	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:142239400-142256400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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