Variant report

Variant	rs6029982
Chromosome Location	chr20:40740500-40740501
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1076666	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs2067084	0.81[EUR][1000 genomes]
rs6016685	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6016686	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6016687	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs6029979	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6029980	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6130038	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs909777	0.86[CHB][hapmap];0.83[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	nsv3381	chr20:39925326-40765696	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:40715800-40757600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:40722800-40747200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr20:40723200-40741400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:40731200-40742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr20:40733800-40742600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr20:40737600-40747800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr20:40739400-40741000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr20:40740000-40740600	Enhancers	Fetal Intestine Large	intestine

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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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