Variant report

Variant	rs12490201
Chromosome Location	chr3:120574683-120574684
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10934533	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12493977	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12498064	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12632316	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12635124	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13314307	0.80[AMR][1000 genomes]
rs13316005	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13323408	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1394960	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403717	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16831962	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16831974	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16831976	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1960320	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2220255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35147415	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4544547	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6438597	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7624337	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7624461	0.83[AMR][1000 genomes]
rs7624738	0.83[AMR][1000 genomes]
rs7646815	0.83[AMR][1000 genomes]
rs7648074	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7652758	0.83[AMR][1000 genomes]
rs9289149	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289150	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9289151	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9818910	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9819192	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9822141	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9824369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9824653	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9826042	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9826303	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9831352	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9831814	0.83[AMR][1000 genomes]
rs9842745	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9843476	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9844059	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9844215	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9852152	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855929	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9855953	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9859729	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9862685	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9868798	0.83[AMR][1000 genomes]
rs9878416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9881138	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1005396	chr3:120460741-120580319	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv829700	chr3:120469191-120675763	Strong transcription Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1012541	chr3:120482402-120580319	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv1014477	chr3:120482402-120583166	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
10	nsv877380	chr3:120522716-120606438	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv524529	chr3:120573295-120578717	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120573600-120575600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:120573800-120574800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
3	chr3:120573800-120575000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr3:120573800-120575200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:120574000-120574800	Enhancers	H9 Cell Line	embryonic stem cell
6	chr3:120574000-120575200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr3:120574000-120575600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:120574000-120575600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr3:120574000-120575600	Enhancers	Osteobl	bone
10	chr3:120574000-120575800	Enhancers	Ovary	ovary
11	chr3:120574200-120575200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:120574400-120575000	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:120574400-120576400	Enhancers	Hela-S3	cervix
14	chr3:120574600-120574800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:120574600-120575000	Enhancers	Brain Hippocampus Middle	brain
16	chr3:120574600-120575000	Flanking Active TSS	HSMMtube	muscle
17	chr3:120574600-120575200	Enhancers	Fetal Stomach	stomach
18	chr3:120574600-120575200	Enhancers	Right Atrium	heart
19	chr3:120574600-120575600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:120574600-120575600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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