Variant report

Variant	rs1077680
Chromosome Location	chr6:39045582-39045583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10305479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10305516	0.91[CEU][hapmap]
rs10305525	0.90[CEU][hapmap]
rs1076734	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12665144	1.00[CEU][hapmap]
rs2268635	0.90[CEU][hapmap]
rs2268636	0.90[CEU][hapmap]
rs2268645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268646	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2268647	0.89[ASN][1000 genomes]
rs2300612	1.00[CEU][hapmap]
rs3765468	0.90[CEU][hapmap];0.86[CHB][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4711574	0.92[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs59902637	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs742761	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs761386	0.97[ASN][1000 genomes]
rs761387	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv528286	chr6:39019503-39060478	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv470815	chr6:39022698-39051694	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv519907	chr6:39032415-39055012	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1031922	chr6:39034484-39060762	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1793081	chr6:39034516-39048562	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39021200-39072000	Weak transcription	Gastric	stomach
2	chr6:39024200-39057800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:39027400-39073000	Weak transcription	Pancreas	Pancrea
4	chr6:39033600-39052200	Weak transcription	Right Ventricle	heart
5	chr6:39036400-39050200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:39042400-39045600	Enhancers	Fetal Heart	heart
7	chr6:39042400-39045800	Enhancers	GM12878-XiMat	blood
8	chr6:39043200-39050200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr6:39043400-39082000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:39044400-39045600	Enhancers	Left Ventricle	heart
11	chr6:39045200-39045600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:39045200-39054000	Weak transcription	Right Atrium	heart

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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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