Variant report

Variant	rs12715048
Chromosome Location	chr3:23425959-23425960
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1027379	0.81[YRI][hapmap]
rs11708160	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs11711072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11715841	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12330479	0.80[YRI][hapmap]
rs12386394	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12715046	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13087861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1353322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1552930	0.81[YRI][hapmap]
rs1692617	0.85[GIH][hapmap]
rs1692622	0.82[JPT][hapmap]
rs2055310	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2133331	0.89[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs2173460	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2359759	0.87[GIH][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs2884731	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3104243	0.85[GIH][hapmap]
rs3111311	0.89[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs3817002	0.89[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs4858069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858074	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858505	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4858509	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4858510	0.81[AMR][1000 genomes]
rs55797660	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58748418	0.83[EUR][1000 genomes]
rs60430884	0.83[EUR][1000 genomes]
rs60632986	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6550756	0.89[GIH][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap];0.86[YRI][hapmap]
rs66649889	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6769173	0.89[GIH][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs6770091	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs6795968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6796840	0.89[GIH][hapmap]
rs6797907	0.89[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6798153	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs6798328	0.81[EUR][1000 genomes]
rs6804123	0.82[YRI][hapmap]
rs6805889	0.88[CEU][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6808513	0.82[YRI][hapmap]
rs704534	0.85[JPT][hapmap]
rs716456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7374774	0.83[ASN][1000 genomes]
rs7612666	0.80[EUR][1000 genomes]
rs7613091	0.89[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs7614667	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7630344	0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs7631334	0.89[GIH][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.89[YRI][hapmap]
rs778460	0.86[YRI][hapmap]
rs778462	0.89[GIH][hapmap]
rs778482	0.87[EUR][1000 genomes]
rs778485	0.83[AFR][1000 genomes]
rs778486	0.83[GIH][hapmap]
rs778487	0.81[AFR][1000 genomes]
rs778494	0.86[YRI][hapmap]
rs778506	0.85[GIH][hapmap];0.85[MKK][hapmap]
rs778508	0.85[GIH][hapmap]
rs778521	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs952134	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9815921	0.80[EUR][1000 genomes]
rs9820922	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9821419	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9826877	0.83[YRI][hapmap]
rs9830388	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs9830392	0.87[EUR][1000 genomes]
rs9836574	0.92[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9839738	0.88[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9859651	0.89[GIH][hapmap]

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	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
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv876624	chr3:23385877-23483536	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv876625	chr3:23390301-23509597	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1012236	chr3:23408427-23469063	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1010032	chr3:23408985-23469063	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23409200-23431800	Weak transcription	Aorta	Aorta
2	chr3:23410800-23426800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:23419000-23426800	Weak transcription	Brain Substantia Nigra	brain
4	chr3:23419200-23429000	Weak transcription	Brain Angular Gyrus	brain
5	chr3:23420000-23433600	Weak transcription	Primary T cells from cord blood	blood
6	chr3:23420400-23427600	Weak transcription	Primary B cells from cord blood	blood
7	chr3:23420600-23428200	Weak transcription	GM12878-XiMat	blood
8	chr3:23422200-23427000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr3:23422800-23426800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:23423200-23426800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr3:23425400-23426000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr3:23425400-23428000	Enhancers	Psoas Muscle	Psoas
13	chr3:23425400-23428000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr3:23425800-23432200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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