Variant report

Variant	rs6130039
Chromosome Location	chr20:40745797-40745798
allele	A/G
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:17)

rs_ID	r²[population]
rs12480505	0.82[YRI][hapmap]
rs12625871	0.80[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16986553	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2206167	0.86[YRI][hapmap]
rs2223422	0.85[CEU][hapmap]
rs6029997	0.83[EUR][1000 genomes]
rs6093610	0.87[CEU][hapmap]
rs6124418	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs6124419	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6124420	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6130040	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6130047	0.90[YRI][hapmap]
rs6130049	0.91[YRI][hapmap]
rs6130051	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6130052	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6130055	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8183826	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[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:13 , 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	chr20:40737600-40747800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr20:40741800-40747200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr20:40742000-40746200	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr20:40742000-40747200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr20:40742200-40746800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:40742200-40747000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr20:40742200-40747000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr20:40742200-40747200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr20:40742400-40747000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr20:40742600-40747200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr20:40745200-40747600	Weak transcription	Brain Anterior Caudate	brain

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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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