Variant report

Variant	rs12496864
Chromosome Location	chr3:46535071-46535072
allele	C/T
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	PAX5	chr3:46535048-46535918	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46532500..46536089-chr3:46537478..46540838,3	K562	blood:
2	chr3:46533897..46536089-chr3:46538396..46540838,2	K562	blood:

Variant related genes	Relation type
RTP3	TF binding region
ENSG00000163825	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10514713	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130093	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130094	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714743	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719033	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489007	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489117	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490169	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496623	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1402151	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2037391	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2280407	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28413725	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3934896	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60986461	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs883739	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46530800-46535200	Enhancers	K562	blood
2	chr3:46530800-46538600	Weak transcription	Pancreas	Pancrea
3	chr3:46531000-46538400	Weak transcription	Lung	lung
4	chr3:46531200-46541600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:46531400-46537400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:46531400-46537400	Weak transcription	Spleen	Spleen
7	chr3:46531400-46540200	Weak transcription	Left Ventricle	heart
8	chr3:46531600-46537200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:46531600-46537200	Weak transcription	Fetal Thymus	thymus
10	chr3:46531600-46537400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:46531800-46537200	Weak transcription	NH-A	brain
12	chr3:46532400-46538400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:46532400-46538400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:46532800-46537200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:46532800-46538000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:46533000-46537200	Weak transcription	NHLF	lung
17	chr3:46533000-46538400	Weak transcription	Right Ventricle	heart
18	chr3:46533000-46544200	Weak transcription	Psoas Muscle	Psoas
19	chr3:46533200-46537200	Weak transcription	HSMMtube	muscle
20	chr3:46533400-46537200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:46533400-46537200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:46533600-46537200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:46533600-46537200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:46533600-46537200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:46533600-46537200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:46533600-46537200	Weak transcription	HMEC	breast
27	chr3:46533600-46537200	Weak transcription	NHDF-Ad	bronchial
28	chr3:46533600-46537200	Weak transcription	NHEK	skin
29	chr3:46533600-46537400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:46533800-46537200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:46533800-46537200	Weak transcription	HSMM	muscle
32	chr3:46534200-46537200	Weak transcription	Dnd41	blood
33	chr3:46534200-46537200	Weak transcription	Osteobl	bone
34	chr3:46534600-46538400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:46535000-46537200	Weak transcription	Liver	Liver
36	chr3:46535000-46538600	Weak transcription	Fetal Intestine Large	intestine

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