Variant report

Variant	rs9844558
Chromosome Location	chr3:23364883-23364884
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	chr3:23360954..23362532-chr3:23363082..23365861,2	MCF-7	breast:
2	chr3:23361011..23363823-chr3:23364424..23367156,3	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1027380	0.97[ASN][1000 genomes]
rs11711630	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11715107	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13087416	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13095887	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13323077	0.83[GIH][hapmap]
rs1390083	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1495133	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1495134	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1552931	0.87[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1695203	0.83[JPT][hapmap]
rs17342342	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17402378	0.86[GIH][hapmap]
rs2036045	0.87[CEU][hapmap]
rs2047340	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2055155	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2088129	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2132145	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2132147	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2132148	0.84[CEU][hapmap]
rs2132149	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2173057	0.83[GIH][hapmap]
rs2201481	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2359760	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36073188	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4293660	0.89[ASN][1000 genomes]
rs4334589	0.89[ASN][1000 genomes]
rs4858065	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858066	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4858488	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858498	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6550751	0.80[AMR][1000 genomes]
rs6769959	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6780388	0.93[YRI][hapmap]
rs6790185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73149661	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7618910	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7635882	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7636532	0.89[ASN][1000 genomes]
rs7648425	1.00[CHB][hapmap];0.84[JPT][hapmap];0.97[ASN][1000 genomes]
rs778463	0.83[GIH][hapmap]
rs778493	1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[EUR][1000 genomes]
rs778502	0.93[YRI][hapmap]
rs778515	0.83[GIH][hapmap]
rs778524	0.84[JPT][hapmap]
rs903519	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs931609	0.83[GIH][hapmap]
rs9631541	0.83[GIH][hapmap]
rs9815299	0.83[GIH][hapmap]
rs9826103	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9836135	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs9840015	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848331	1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs9862734	0.84[JPT][hapmap]
rs9875910	0.86[GIH][hapmap]

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	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1004417	chr3:23318797-23389422	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23350600-23366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:23355200-23365400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:23355800-23366000	Weak transcription	Ovary	ovary
4	chr3:23356800-23365400	Weak transcription	Brain Anterior Caudate	brain
5	chr3:23356800-23367600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:23357000-23378800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:23357600-23366600	Weak transcription	Brain Substantia Nigra	brain
8	chr3:23357800-23366000	Weak transcription	HSMM	muscle
9	chr3:23358400-23366400	Weak transcription	HSMMtube	muscle
10	chr3:23359200-23366000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr3:23361600-23365200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:23361600-23365800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:23361600-23366400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:23362800-23366000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:23363000-23366400	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:23363200-23365200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:23363200-23371000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:23363400-23365200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:23363800-23371000	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:23364000-23365800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:23364800-23366400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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