Variant report

Variant	rs12990828
Chromosome Location	chr2:40271833-40271834
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10084468	1.00[ASN][1000 genomes]
rs10171743	1.00[EUR][1000 genomes]
rs10186088	1.00[ASN][1000 genomes]
rs10193939	1.00[EUR][1000 genomes]
rs10198341	0.92[EUR][1000 genomes]
rs11124722	0.92[EUR][1000 genomes]
rs11124728	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124731	1.00[EUR][1000 genomes]
rs11124732	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1117015	1.00[EUR][1000 genomes]
rs12468162	1.00[ASN][1000 genomes]
rs12468217	1.00[EUR][1000 genomes]
rs12471474	1.00[EUR][1000 genomes]
rs12476283	1.00[EUR][1000 genomes]
rs12712674	1.00[EUR][1000 genomes]
rs13010575	1.00[EUR][1000 genomes]
rs13035505	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13427221	1.00[EUR][1000 genomes]
rs1548875	0.92[EUR][1000 genomes]
rs1861253	0.92[EUR][1000 genomes]
rs1861262	1.00[EUR][1000 genomes]
rs2024418	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2024419	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2192721	1.00[EUR][1000 genomes]
rs2215970	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2215978	1.00[EUR][1000 genomes]
rs2215979	1.00[EUR][1000 genomes]
rs2373785	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2373786	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3944017	1.00[EUR][1000 genomes]
rs4245781	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670985	0.92[EUR][1000 genomes]
rs4952629	1.00[EUR][1000 genomes]
rs4952639	1.00[EUR][1000 genomes]
rs58460675	1.00[EUR][1000 genomes]
rs6544283	0.92[EUR][1000 genomes]
rs6544286	1.00[EUR][1000 genomes]
rs6544289	1.00[ASN][1000 genomes]
rs6544292	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544299	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544300	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6544304	1.00[EUR][1000 genomes]
rs6712057	1.00[EUR][1000 genomes]
rs6732101	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs6732448	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6733262	1.00[EUR][1000 genomes]
rs6747284	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72934813	0.92[EUR][1000 genomes]
rs72938756	0.92[EUR][1000 genomes]
rs757643	1.00[MEX][hapmap]
rs7583651	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586599	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589081	0.92[EUR][1000 genomes]
rs7591903	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs917972	0.92[EUR][1000 genomes]
rs917978	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs917979	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs917981	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9749791	0.92[EUR][1000 genomes]
rs981009	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916300	chr2:40079899-40339019	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv873899	chr2:40161168-40281964	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1009532	chr2:40165606-40291224	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv535653	chr2:40165606-40291224	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873900	chr2:40202505-40278909	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv581501	chr2:40256218-40285145	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40269400-40299200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:40270200-40272000	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr2:40270200-40272000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:40270200-40272200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:40270800-40275400	Weak transcription	HSMM	muscle
6	chr2:40271000-40276400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:40271400-40272600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:40271800-40275600	Weak transcription	NHDF-Ad	bronchial

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