Variant report

Variant	rs793482
Chromosome Location	chr3:99489397-99489398
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11719468	0.85[YRI][hapmap]
rs1711564	0.82[LWK][hapmap];0.85[YRI][hapmap]
rs1718235	0.86[LWK][hapmap];0.92[YRI][hapmap]
rs1718240	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.87[ASN][1000 genomes]
rs2449106	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs4244712	0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap]
rs4928230	0.82[YRI][hapmap]
rs634861	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs669676	0.84[ASW][hapmap];0.86[LWK][hapmap];0.85[YRI][hapmap]
rs681819	0.81[CEU][hapmap]
rs704572	0.90[YRI][hapmap];0.90[AFR][1000 genomes]
rs7650727	0.82[YRI][hapmap]
rs793439	0.82[YRI][hapmap]
rs793450	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs793469	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs793498	0.91[ASN][1000 genomes]
rs793502	0.86[LWK][hapmap];0.92[YRI][hapmap]
rs813218	0.86[LWK][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877217	chr3:99418950-99496351	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv508231	chr3:99442020-99498951	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs793482	SENP7	cis	parietal	SCAN
rs793482	C3orf26	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99462400-99495600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:99472400-99493000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:99472400-99493000	Weak transcription	NHEK	skin
4	chr3:99472400-99493400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:99482400-99493000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:99484400-99493200	Weak transcription	Adipose Nuclei	Adipose
7	chr3:99484400-99493400	Weak transcription	Aorta	Aorta
8	chr3:99484400-99500400	Weak transcription	HSMMtube	muscle
9	chr3:99485200-99493200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:99485200-99493200	Weak transcription	NH-A	brain
11	chr3:99485200-99493200	Weak transcription	NHLF	lung
12	chr3:99485200-99493400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:99485800-99489600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:99486800-99493000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:99487600-99489600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:99487600-99493000	Weak transcription	NHDF-Ad	bronchial
17	chr3:99488200-99493400	Weak transcription	HUVEC	blood vessel
18	chr3:99488400-99489400	Weak transcription	HSMM	muscle
19	chr3:99488400-99493200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:99488400-99493200	Weak transcription	Osteobl	bone

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