Variant report

Variant	rs4894200
Chromosome Location	chr2:177634107-177634108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10930752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11889984	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467333	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12469087	0.83[CEU][hapmap];0.82[CHB][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12611718	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs12618099	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2221939	0.83[CEU][hapmap]
rs4021394	0.94[CEU][hapmap];0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4600700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4894197	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[GIH][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4894198	0.82[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs6706063	1.00[CEU][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs6706426	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6758766	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][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	nsv527737	chr2:177538266-177692572	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv583686	chr2:177538266-177692572	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006500	chr2:177548521-177707097	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4894200	LOC100130691	cis	parietal	SCAN
rs4894200	HOXD11	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177623400-177634400	Weak transcription	Right Atrium	heart
2	chr2:177628800-177655400	Weak transcription	Ovary	ovary
3	chr2:177631200-177638400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:177632800-177634600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr2:177633000-177634400	Enhancers	Fetal Thymus	thymus
6	chr2:177633400-177635600	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:177633800-177634600	Enhancers	Psoas Muscle	Psoas
8	chr2:177634000-177634600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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