Variant report

Variant	rs778484
Chromosome Location	chr3:23432228-23432229
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:23432120-23432270	GM12871	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000228171	TF binding region

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1027379	0.80[ASN][1000 genomes]
rs11129116	0.80[ASN][1000 genomes]
rs11129119	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11718082	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11916411	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11918529	1.00[CEU][hapmap]
rs12497974	0.82[ASN][1000 genomes]
rs12715047	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13064035	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13321359	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13326048	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1498809	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1498811	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1532355	0.82[ASN][1000 genomes]
rs1692612	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1692617	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1692620	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1692622	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs1692650	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1692651	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1692652	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1695170	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1695171	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1695181	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1695200	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17194786	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1874235	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1908773	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2036226	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2359759	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2359763	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3104243	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3104244	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34080387	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4241512	0.81[EUR][1000 genomes]
rs4513393	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs4635650	0.81[EUR][1000 genomes]
rs4858071	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858072	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4858077	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858497	0.82[ASN][1000 genomes]
rs4858500	0.80[ASN][1000 genomes]
rs4858501	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4858502	0.82[AMR][1000 genomes]
rs4858504	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4858506	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858508	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858511	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60581845	0.89[EUR][1000 genomes]
rs6550756	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6763329	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6763535	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6767599	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6769173	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6775232	0.90[EUR][1000 genomes]
rs6776424	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6780723	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6780787	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6784195	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6796840	0.96[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6808513	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs704533	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs704534	0.85[EUR][1000 genomes]
rs716457	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7631334	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7634117	0.85[EUR][1000 genomes]
rs7640308	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7644666	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7645209	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs778459	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778460	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778461	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778462	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778467	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs778468	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778470	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778471	0.82[CEU][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs778475	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778476	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778480	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778485	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778486	0.92[CEU][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778487	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778488	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778494	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs778496	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs778499	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs778500	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs778501	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs778503	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778506	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778507	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778508	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs778510	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs778514	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs778523	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778526	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9824359	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9825778	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9826089	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9826647	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9827507	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9830742	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9840820	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9849424	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9854148	0.80[AMR][1000 genomes]
rs9856169	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9859515	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9859651	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9873317	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9874082	0.80[AMR][1000 genomes]
rs9874519	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9874822	0.80[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	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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23420000-23433600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:23427000-23445000	Weak transcription	Right Ventricle	heart
3	chr3:23428600-23435400	Weak transcription	Brain Substantia Nigra	brain
4	chr3:23429800-23445400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:23430800-23433400	Weak transcription	Fetal Heart	heart
6	chr3:23431000-23436200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:23431400-23432400	Enhancers	GM12878-XiMat	blood
8	chr3:23431400-23436200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:23431400-23436400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:23431400-23447800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:23431600-23432400	Enhancers	Spleen	Spleen
12	chr3:23431600-23435800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr3:23431600-23436000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:23431800-23432400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:23431800-23433000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:23431800-23435600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:23431800-23436000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:23432000-23433400	Weak transcription	Primary B cells from cord blood	blood
19	chr3:23432000-23434400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:23432000-23438000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:23432200-23432400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:23432200-23433000	Enhancers	Liver	Liver
23	chr3:23432200-23433200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:23432200-23433800	Weak transcription	Psoas Muscle	Psoas
25	chr3:23432200-23452600	Weak transcription	Aorta	Aorta

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