Variant report

Variant	rs3800199
Chromosome Location	chr6:132050585-132050586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10457575	0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12192518	0.84[CHB][hapmap]
rs12199015	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12199875	0.82[ASN][1000 genomes]
rs12204520	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs12206403	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12206779	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207523	0.86[CHD][hapmap];0.83[TSI][hapmap]
rs12210900	0.94[CHB][hapmap];0.80[ASN][1000 genomes]
rs12530416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17060552	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs2270089	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2286453	0.90[CHB][hapmap]
rs28671630	0.92[ASN][1000 genomes]
rs3213693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3213694	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs365475	0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3778571	0.81[ASN][1000 genomes]
rs3800193	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs3800194	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs3800195	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs3800198	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3800200	0.99[ASN][1000 genomes]
rs3843996	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3850247	0.80[ASN][1000 genomes]
rs3850249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3861467	0.93[ASN][1000 genomes]
rs3861468	0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3904056	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4126646	0.80[ASN][1000 genomes]
rs4897536	0.99[ASN][1000 genomes]
rs55931014	0.80[ASN][1000 genomes]
rs60507180	0.89[ASN][1000 genomes]
rs6569753	0.85[CHB][hapmap]
rs6901900	0.95[CHB][hapmap]
rs6908953	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6909448	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[ASN][1000 genomes]
rs6922673	0.80[ASN][1000 genomes]
rs6931997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6941622	0.92[ASN][1000 genomes]
rs73001214	0.80[ASN][1000 genomes]
rs73554727	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7738667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7745372	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7746945	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7762879	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs7765347	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9321308	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs9483311	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs9483321	0.95[CHB][hapmap]
rs9483334	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9483335	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9493038	0.83[CHB][hapmap]
rs9493048	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs9493050	0.95[CHB][hapmap];0.84[CHD][hapmap]
rs9493057	0.82[ASN][1000 genomes]
rs9493081	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9493082	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9493083	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9493084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv515476	chr6:131615425-132228577	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv7968	chr6:131917172-132321099	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv830809	chr6:131953928-132126417	Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv830810	chr6:131960923-132138396	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	nsv886669	chr6:131991532-132059074	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131998600-132054000	Weak transcription	Fetal Intestine Small	intestine
2	chr6:132002600-132054400	Weak transcription	K562	blood
3	chr6:132040600-132063200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr6:132044200-132055400	Weak transcription	Colonic Mucosa	Colon
5	chr6:132044800-132054400	Weak transcription	Fetal Intestine Large	intestine
6	chr6:132048000-132054600	Weak transcription	Adipose Nuclei	Adipose
7	chr6:132048000-132057200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:132048200-132065200	Weak transcription	Liver	Liver
9	chr6:132048400-132065200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:132048600-132054400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr6:132048800-132051000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:132048800-132051600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:132049000-132051200	Enhancers	Osteobl	bone
14	chr6:132049000-132051600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:132049400-132051000	Enhancers	HSMM	muscle
16	chr6:132049800-132054600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:132050200-132050600	Weak transcription	HepG2	liver
18	chr6:132050400-132052600	Weak transcription	Muscle Satellite Cultured Cells	--

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