Variant report

Variant	rs9875299
Chromosome Location	chr3:139724111-139724112
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:139721983..139724964-chr3:139726808..139729400,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1157880	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs11712956	1.00[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13080287	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs2012477	0.95[ASN][1000 genomes]
rs2012512	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs2114165	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs2114166	1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs2162210	0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs2162211	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs2882368	1.00[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs34053368	0.95[ASN][1000 genomes]
rs34903090	0.95[ASN][1000 genomes]
rs6766139	0.90[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs6766209	0.95[ASN][1000 genomes]
rs6766312	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs6768805	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs6769344	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7621988	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs7627845	0.89[ASN][1000 genomes]
rs7632475	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7640131	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7641534	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7641861	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7641890	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7642085	0.90[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs7653609	0.95[ASN][1000 genomes]
rs9289593	0.95[ASN][1000 genomes]
rs9815854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818660	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9828110	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9830596	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9833439	0.91[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9834731	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs9835073	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9840271	1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs9841389	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9845106	0.91[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs9845526	0.95[ASN][1000 genomes]
rs9845932	0.82[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.85[ASN][1000 genomes]
rs9850893	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9852676	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9853746	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9855298	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9856121	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9862536	0.81[CHB][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs9863029	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9864281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9866483	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs9871885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9873448	0.95[ASN][1000 genomes]
rs9878784	0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]

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	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv998423	chr3:139526446-139947336	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv829738	chr3:139670836-139851945	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139682600-139726000	Weak transcription	HSMMtube	muscle
2	chr3:139714400-139741200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:139722200-139733400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:139723200-139724200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:139723200-139725600	Enhancers	Ovary	ovary
6	chr3:139724000-139724200	Enhancers	Pancreas	Pancrea
7	chr3:139724000-139727800	Enhancers	Fetal Muscle Leg	muscle

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