Variant report

Variant	rs12489007
Chromosome Location	chr3:46545408-46545409
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46539462..46541927-chr3:46542900..46546171,3	K562	blood:
2	chr3:46539335..46541927-chr3:46542072..46545650,5	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10514713	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714743	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719033	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489117	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12490169	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496623	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12496864	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1402151	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037391	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2139634	0.80[EUR][1000 genomes]
rs2280407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28413725	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3934896	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60986461	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6763280	0.80[EUR][1000 genomes]
rs883739	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46537200-46546200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:46537200-46547000	Enhancers	Fetal Thymus	thymus
3	chr3:46537200-46550200	Enhancers	K562	blood
4	chr3:46538200-46546800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:46538800-46546600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:46538800-46546800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:46539000-46547200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:46539200-46547600	Weak transcription	Spleen	Spleen
9	chr3:46541000-46557600	Weak transcription	Left Ventricle	heart
10	chr3:46541000-46580200	Weak transcription	Fetal Heart	heart
11	chr3:46541200-46562200	Weak transcription	Right Ventricle	heart
12	chr3:46541600-46545600	Enhancers	Fetal Muscle Leg	muscle
13	chr3:46541600-46545600	Enhancers	HSMM	muscle
14	chr3:46542000-46545600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:46542000-46547000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:46542200-46545600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr3:46542200-46545800	Enhancers	HSMMtube	muscle
18	chr3:46543400-46547400	Weak transcription	Primary B cells from cord blood	blood
19	chr3:46544000-46545600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:46544000-46545600	Enhancers	Fetal Muscle Trunk	muscle
21	chr3:46544200-46545600	Enhancers	Primary T cells from cord blood	blood
22	chr3:46544400-46545600	Enhancers	Dnd41	blood
23	chr3:46544400-46545600	ZNF genes & repeats	GM12878-XiMat	blood
24	chr3:46544600-46545600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr3:46544800-46556000	Weak transcription	Psoas Muscle	Psoas
26	chr3:46544800-46599400	Weak transcription	Right Atrium	heart
27	chr3:46545000-46547200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:46545000-46547200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:46545200-46545600	Enhancers	Osteobl	bone
30	chr3:46545400-46545600	Enhancers	NHDF-Ad	bronchial
31	chr3:46545400-46547600	Weak transcription	Ovary	ovary
32	chr3:46545400-46551200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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