Variant report

Variant	rs12490169
Chromosome Location	chr3:46547400-46547401
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46528809..46531447-chr3:46546904..46549677,2	K562	blood:
2	chr3:46547294..46549950-chr3:46554092..46556061,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10514713	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10865941	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs11130093	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130094	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714743	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719033	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489007	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489117	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12496623	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496864	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1402151	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1520483	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs17030627	0.84[AFR][1000 genomes]
rs2037391	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2139634	0.80[EUR][1000 genomes]
rs2280407	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28413725	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3934896	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60986461	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763280	0.80[EUR][1000 genomes]
rs883739	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs885485	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs885486	1.00[CEU][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46537200-46550200	Enhancers	K562	blood
2	chr3:46539200-46547600	Weak transcription	Spleen	Spleen
3	chr3:46541000-46557600	Weak transcription	Left Ventricle	heart
4	chr3:46541000-46580200	Weak transcription	Fetal Heart	heart
5	chr3:46541200-46562200	Weak transcription	Right Ventricle	heart
6	chr3:46543400-46547400	Weak transcription	Primary B cells from cord blood	blood
7	chr3:46544800-46556000	Weak transcription	Psoas Muscle	Psoas
8	chr3:46544800-46599400	Weak transcription	Right Atrium	heart
9	chr3:46545400-46547600	Weak transcription	Ovary	ovary
10	chr3:46545400-46551200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:46545600-46558000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:46545600-46559200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:46546200-46547400	Enhancers	HSMMtube	muscle
14	chr3:46546600-46548200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:46546800-46548000	Enhancers	Fetal Muscle Trunk	muscle
16	chr3:46546800-46548200	Enhancers	H9 Cell Line	embryonic stem cell
17	chr3:46546800-46548200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:46546800-46548400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:46547000-46547800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:46547000-46548000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:46547000-46548000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:46547000-46548200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr3:46547000-46549400	Weak transcription	Fetal Thymus	thymus
24	chr3:46547200-46547800	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:46547200-46548000	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:46547200-46548000	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr3:46547200-46548000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:46547200-46548200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr3:46547400-46548000	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr3:46547400-46552600	Weak transcription	HSMMtube	muscle

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