Variant report

Variant	rs6799764
Chromosome Location	chr3:140287939-140287940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10755093	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10804675	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10804676	0.89[ASN][1000 genomes]
rs10935386	0.92[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs10935387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714465	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11916215	0.92[CHB][hapmap];0.87[ASN][1000 genomes]
rs11924925	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11924952	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494698	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078522	0.87[GIH][hapmap];0.88[MEX][hapmap]
rs347973	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs347975	0.86[EUR][1000 genomes]
rs4683508	0.81[EUR][1000 genomes]
rs4683509	0.92[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs6775380	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6803516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9845717	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757891	chr3:139925764-140524730	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2759181	chr3:139925764-140524730	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv527831	chr3:139932966-140533823	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv34489	chr3:140009020-140469302	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2757012	chr3:140009220-140460228	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv870185	chr3:140265153-140395673	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6799764	C3orf58	cis	parietal	SCAN
rs6799764	ZBTB38	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140279200-140288400	Strong transcription	HSMMtube	muscle
2	chr3:140279600-140289600	Weak transcription	Fetal Brain Female	brain
3	chr3:140282800-140288000	Weak transcription	Liver	Liver
4	chr3:140286200-140292800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:140286200-140295000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:140287600-140288200	Enhancers	Left Ventricle	heart
7	chr3:140287600-140288200	Enhancers	Right Atrium	heart
8	chr3:140287600-140288400	Enhancers	Brain Hippocampus Middle	brain
9	chr3:140287600-140288400	Enhancers	Ovary	ovary
10	chr3:140287600-140288600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:140287600-140288600	Enhancers	Adipose Nuclei	Adipose
12	chr3:140287600-140289000	Enhancers	Psoas Muscle	Psoas
13	chr3:140287800-140288000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:140287800-140288200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:140287800-140288400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:140287800-140288400	Enhancers	Brain Anterior Caudate	brain
17	chr3:140287800-140288400	Enhancers	Fetal Lung	lung
18	chr3:140287800-140288400	Enhancers	Pancreas	Pancrea
19	chr3:140287800-140289000	Enhancers	Skeletal Muscle Female	skeletal 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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