Variant report

Variant	rs6429896
Chromosome Location	chr2:142251434-142251435
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10165979	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10167487	0.89[YRI][hapmap]
rs10176397	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10176693	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10187180	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10191434	0.87[YRI][hapmap]
rs10200529	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10200578	0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10200782	1.00[AMR][1000 genomes]
rs10200845	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1038346	0.89[YRI][hapmap]
rs11887261	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11904458	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12466189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12472734	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12617980	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12618575	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12691613	0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12691614	1.00[AMR][1000 genomes]
rs12691615	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1483138	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1483152	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2128694	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2170667	1.00[AMR][1000 genomes]
rs2381110	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381111	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381112	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381113	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2381192	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3856360	0.89[YRI][hapmap]
rs3935992	1.00[AMR][1000 genomes]
rs4008531	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4245859	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4264515	1.00[AMR][1000 genomes]
rs4296372	0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4359580	0.89[YRI][hapmap];0.88[AFR][1000 genomes]
rs4366842	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4396652	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4439901	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4441406	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4446017	1.00[YRI][hapmap]
rs4476294	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4477847	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4482418	0.89[YRI][hapmap];0.86[AFR][1000 genomes]
rs4482419	0.84[AFR][1000 genomes]
rs4555282	1.00[AMR][1000 genomes]
rs4954909	1.00[AMR][1000 genomes]
rs4954913	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5001568	1.00[YRI][hapmap]
rs6429897	1.00[AFR][1000 genomes]
rs6429901	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6429902	1.00[AMR][1000 genomes]
rs6706356	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6706377	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6707422	0.89[YRI][hapmap]
rs6707441	0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6708438	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6710020	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6713043	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6718844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6737585	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6749472	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7557631	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7571511	1.00[AFR][1000 genomes]
rs7572480	1.00[AMR][1000 genomes]
rs7582623	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7585325	1.00[AMR][1000 genomes]
rs7590820	0.89[YRI][hapmap]
rs7593866	1.00[AMR][1000 genomes]
rs7607376	1.00[AMR][1000 genomes]
rs983197	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs983198	0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs983199	0.88[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	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
4	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
5	nsv875243	chr2:142219033-142259592	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
6	nsv459607	chr2:142226768-142263400	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
7	nsv583207	chr2:142226768-142263400	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	nsv459618	chr2:142246988-142263746	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
9	nsv583209	chr2:142246988-142263746	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:8 , 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
2	chr2:142247800-142266200	Weak transcription	Brain Anterior Caudate	brain
3	chr2:142249600-142254800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:142249600-142257600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:142250000-142255000	Weak transcription	NH-A	brain
6	chr2:142250200-142254800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:142251000-142251800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:142251000-142251800	Enhancers	Esophagus	oesophagus

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