Variant report

Variant	rs6802358
Chromosome Location	chr3:143166660-143166661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1525010	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1525011	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs1723034	0.95[CHB][hapmap];0.86[CHD][hapmap]
rs2582353	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2582354	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs59466501	0.83[ASN][1000 genomes]
rs59667799	0.84[ASN][1000 genomes]
rs61591068	0.83[ASN][1000 genomes]
rs67392581	0.94[ASN][1000 genomes]
rs6780280	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs6804097	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs838610	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs838612	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs838614	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs838615	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs838617	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs838619	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs838621	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap]
rs838624	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs838626	0.95[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs838629	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs838640	0.91[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]

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	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	esv2757894	chr3:142992697-143285979	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2759184	chr3:142992697-143285979	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6802358	RNF7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143155800-143169800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:143159600-143200800	Weak transcription	Esophagus	oesophagus
3	chr3:143162600-143169800	Weak transcription	Brain Substantia Nigra	brain
4	chr3:143162800-143167600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:143163400-143167200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:143163400-143181400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:143163400-143196800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:143163600-143169800	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:143163600-143184000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:143163600-143187000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:143163800-143170600	Weak transcription	Fetal Lung	lung
12	chr3:143163800-143183600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:143163800-143196400	Weak transcription	Fetal Stomach	stomach
14	chr3:143163800-143203400	Weak transcription	Ovary	ovary
15	chr3:143164000-143175000	Weak transcription	Primary T cells from cord blood	blood
16	chr3:143164600-143169400	Weak transcription	GM12878-XiMat	blood
17	chr3:143164600-143169600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:143164600-143169600	Weak transcription	Primary B cells from cord blood	blood
19	chr3:143164800-143169600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr3:143164800-143169600	Weak transcription	Monocytes-CD14+_RO01746	blood

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