Variant report

Variant	rs9841642
Chromosome Location	chr3:180000733-180000734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10513775	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11919129	1.00[EUR][1000 genomes]
rs11923122	1.00[EUR][1000 genomes]
rs11924444	1.00[EUR][1000 genomes]
rs11929056	1.00[EUR][1000 genomes]
rs13320643	1.00[EUR][1000 genomes]
rs13320900	1.00[EUR][1000 genomes]
rs13324315	1.00[EUR][1000 genomes]
rs13327114	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13327183	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1543266	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16831253	1.00[EUR][1000 genomes]
rs16831270	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1965540	0.84[AFR][1000 genomes]
rs2090762	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs2091272	0.84[YRI][hapmap]
rs28373443	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28377416	1.00[EUR][1000 genomes]
rs28545820	1.00[EUR][1000 genomes]
rs28623139	1.00[EUR][1000 genomes]
rs28701054	1.00[EUR][1000 genomes]
rs28726303	1.00[EUR][1000 genomes]
rs28736488	1.00[EUR][1000 genomes]
rs28758960	1.00[EUR][1000 genomes]
rs2879655	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28818282	1.00[EUR][1000 genomes]
rs4499599	1.00[EUR][1000 genomes]
rs4621328	1.00[EUR][1000 genomes]
rs56406807	1.00[EUR][1000 genomes]
rs57727445	1.00[EUR][1000 genomes]
rs60008753	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6765080	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6765816	0.94[AFR][1000 genomes]
rs6765906	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6772673	1.00[EUR][1000 genomes]
rs6776289	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6779403	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6784007	1.00[EUR][1000 genomes]
rs6787700	1.00[EUR][1000 genomes]
rs6795109	1.00[EUR][1000 genomes]
rs6797862	1.00[EUR][1000 genomes]
rs6800776	0.82[YRI][hapmap]
rs6803803	1.00[EUR][1000 genomes]
rs6804532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6809894	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73883804	1.00[EUR][1000 genomes]
rs73883810	1.00[EUR][1000 genomes]
rs73883833	1.00[EUR][1000 genomes]
rs73885453	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73885465	1.00[EUR][1000 genomes]
rs73885473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73885496	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7612350	1.00[EUR][1000 genomes]
rs7614651	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7628443	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7635460	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7643125	1.00[EUR][1000 genomes]
rs7646970	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9290693	1.00[EUR][1000 genomes]
rs9290694	1.00[EUR][1000 genomes]
rs9290698	1.00[EUR][1000 genomes]
rs9815044	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9818567	1.00[EUR][1000 genomes]
rs9819315	1.00[EUR][1000 genomes]
rs9825264	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9825542	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9826576	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9827331	1.00[EUR][1000 genomes]
rs9828833	1.00[EUR][1000 genomes]
rs9830454	1.00[EUR][1000 genomes]
rs9830623	1.00[EUR][1000 genomes]
rs9832076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833910	1.00[EUR][1000 genomes]
rs9836941	1.00[EUR][1000 genomes]
rs9841268	1.00[EUR][1000 genomes]
rs9841905	1.00[EUR][1000 genomes]
rs9842405	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9844266	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9844627	1.00[EUR][1000 genomes]
rs9844929	1.00[EUR][1000 genomes]
rs9845131	1.00[EUR][1000 genomes]
rs9846836	1.00[EUR][1000 genomes]
rs9849568	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9852228	1.00[EUR][1000 genomes]
rs9856995	1.00[EUR][1000 genomes]
rs9858982	1.00[EUR][1000 genomes]
rs9859460	1.00[EUR][1000 genomes]
rs9861136	1.00[EUR][1000 genomes]
rs9862085	1.00[EUR][1000 genomes]
rs9863397	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9863949	1.00[EUR][1000 genomes]
rs9866861	1.00[EUR][1000 genomes]
rs9871675	1.00[EUR][1000 genomes]
rs9872191	1.00[EUR][1000 genomes]
rs9872323	1.00[EUR][1000 genomes]
rs9872365	1.00[EUR][1000 genomes]
rs9873559	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9877145	1.00[EUR][1000 genomes]
rs9884094	1.00[EUR][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	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv878041	chr3:179983857-180097855	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179993000-180002000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:179998800-180001200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:179998800-180001600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:179998800-180002400	Weak transcription	HMEC	breast
5	chr3:179998800-180002600	Weak transcription	NHLF	lung
6	chr3:179999000-180001200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:180000000-180002000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:180000200-180003600	Enhancers	NHDF-Ad	bronchial

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