Variant report

Variant	rs12330479
Chromosome Location	chr3:23279623-23279624
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1013460	0.88[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1027379	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs1032499	0.89[JPT][hapmap]
rs11129113	0.80[ASN][1000 genomes]
rs11129116	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs11708117	0.85[AFR][1000 genomes]
rs11708176	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11717397	0.82[ASN][1000 genomes]
rs11720461	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12330262	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12493361	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs12496983	0.83[ASN][1000 genomes]
rs12629848	0.88[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12715048	0.80[YRI][hapmap]
rs13074192	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs13080261	0.91[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13080401	0.88[ASN][1000 genomes]
rs13081371	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13326048	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1353322	0.92[YRI][hapmap]
rs1552930	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1692617	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs1692651	0.82[CHB][hapmap]
rs1695171	0.82[CHB][hapmap]
rs17012812	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs17012869	0.88[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1973400	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2055154	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2172828	0.88[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2359759	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2359763	0.82[CHB][hapmap]
rs2884731	0.80[YRI][hapmap]
rs3104243	0.81[CHB][hapmap]
rs34919006	0.91[ASN][1000 genomes]
rs4241511	0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4488778	0.82[AFR][1000 genomes]
rs4858062	0.88[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4858064	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4858074	0.80[YRI][hapmap]
rs4858483	0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4858484	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4858491	0.85[ASN][1000 genomes]
rs4858492	0.83[ASN][1000 genomes]
rs4858496	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs4858497	0.88[CHB][hapmap]
rs4858500	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs4858502	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs4858506	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs59429714	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6550746	0.85[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs6550748	0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6550755	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs6550756	0.81[CHB][hapmap];0.83[YRI][hapmap]
rs6769173	0.81[CHB][hapmap]
rs6784195	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6784771	0.88[CHB][hapmap];0.83[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6795492	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6795968	0.80[YRI][hapmap]
rs6796840	0.81[CHB][hapmap]
rs6804123	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs6805889	0.88[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs716457	0.81[CHB][hapmap]
rs7429470	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7617072	0.88[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7622784	0.89[ASN][1000 genomes]
rs7631334	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs778459	0.82[CHB][hapmap]
rs778460	0.82[CHB][hapmap]
rs778462	0.81[CHB][hapmap]
rs778468	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs778470	0.82[CHB][hapmap]
rs778471	0.82[CHB][hapmap]
rs778486	0.81[CHB][hapmap]
rs778494	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs778506	0.81[CHB][hapmap]
rs778508	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9310715	0.88[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs952134	0.84[YRI][hapmap]
rs9809176	0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9816895	0.86[ASN][1000 genomes]
rs9821101	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9825778	0.94[JPT][hapmap]
rs9826647	0.82[CHB][hapmap]
rs9826877	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9836787	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9839738	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs9841123	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9841944	0.89[ASN][1000 genomes]
rs9846398	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9847027	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs9847958	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9848077	0.88[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9849176	0.82[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs9853489	0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs9854590	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9859651	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs9861803	0.88[AFR][1000 genomes]
rs9864908	0.82[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9865602	0.85[ASN][1000 genomes]
rs9874082	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs9881332	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23265400-23282000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:23272600-23283000	Weak transcription	HMEC	breast
3	chr3:23274400-23280800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:23274600-23279800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:23274600-23281400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:23274600-23283000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:23274800-23280200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:23274800-23298200	Weak transcription	Aorta	Aorta
9	chr3:23275000-23280800	Weak transcription	Brain Anterior Caudate	brain
10	chr3:23276800-23281000	Weak transcription	Fetal Heart	heart
11	chr3:23277400-23279800	Weak transcription	Psoas Muscle	Psoas
12	chr3:23277400-23280800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:23278000-23280200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:23278400-23279800	Weak transcription	Brain Substantia Nigra	brain
15	chr3:23278400-23280000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr3:23278400-23280000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:23278400-23280800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:23278400-23280800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:23278600-23279800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:23278600-23279800	Weak transcription	Brain Angular Gyrus	brain
21	chr3:23278600-23280200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:23278600-23280200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr3:23278600-23281200	Weak transcription	Adipose Nuclei	Adipose
24	chr3:23278600-23289600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:23278800-23283000	Weak transcription	Left Ventricle	heart
26	chr3:23279400-23282800	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr3:23279600-23280200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:23279600-23280400	Enhancers	Brain Hippocampus Middle	brain
29	chr3:23279600-23281200	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr3:23279600-23281600	Enhancers	Brain Inferior Temporal Lobe	brain

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