Variant report

Variant	rs3024389
Chromosome Location	chr6:6249620-6249621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13196774	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17141883	1.00[JPT][hapmap]
rs17141887	1.00[JPT][hapmap]
rs3024358	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3024362	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3024365	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3024370	0.83[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3024378	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3024380	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3024381	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3024382	1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3024387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3895270	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3895271	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4959375	1.00[JPT][hapmap]
rs6597197	0.96[CEU][hapmap];0.90[GIH][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7744744	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7769467	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883421	chr6:6163492-6574384	Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv883422	chr6:6163492-6769930	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 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	chr6:6223600-6251600	Weak transcription	HSMM	muscle
2	chr6:6247200-6249800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:6247600-6250400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr6:6247600-6250800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:6249600-6250400	Strong transcription	HSMMtube	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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