Variant report

Variant	rs4952629
Chromosome Location	chr2:40261228-40261229
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10171743	1.00[EUR][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]
rs11124731	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11124732	1.00[EUR][1000 genomes]
rs1117015	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12468217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12471474	1.00[EUR][1000 genomes]
rs12476283	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12712674	1.00[EUR][1000 genomes]
rs12990828	1.00[EUR][1000 genomes]
rs13010575	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];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	1.00[EUR][1000 genomes]
rs2024419	1.00[EUR][1000 genomes]
rs2192721	1.00[EUR][1000 genomes]
rs2215970	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2215978	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2215979	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2373785	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2373786	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3944017	1.00[EUR][1000 genomes]
rs4245781	1.00[EUR][1000 genomes]
rs4670985	0.92[EUR][1000 genomes]
rs4952639	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58460675	1.00[EUR][1000 genomes]
rs6544283	0.92[EUR][1000 genomes]
rs6544286	1.00[EUR][1000 genomes]
rs6544292	0.85[EUR][1000 genomes]
rs6544299	1.00[EUR][1000 genomes]
rs6544300	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6544304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6712057	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6732101	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6732448	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6733262	1.00[EUR][1000 genomes]
rs6747284	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs72934813	0.92[EUR][1000 genomes]
rs72938756	0.92[EUR][1000 genomes]
rs7565203	1.00[EUR][1000 genomes]
rs7583651	1.00[EUR][1000 genomes]
rs7586599	1.00[EUR][1000 genomes]
rs7589081	0.92[EUR][1000 genomes]
rs7591903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7600823	1.00[EUR][1000 genomes]
rs917972	0.92[EUR][1000 genomes]
rs917978	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs917979	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs917981	1.00[EUR][1000 genomes]
rs9749791	0.92[EUR][1000 genomes]
rs981009	1.00[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	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	nsv962063	chr2:40205436-40263295	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	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
9	nsv873901	chr2:40207338-40264861	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	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
11	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

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40258400-40263000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:40258600-40261800	Enhancers	HSMM	muscle
3	chr2:40258600-40261800	Enhancers	Osteobl	bone
4	chr2:40258600-40262000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:40258600-40262200	Enhancers	NHDF-Ad	bronchial
6	chr2:40259200-40262400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr2:40259200-40262400	Enhancers	HMEC	breast
8	chr2:40259400-40261400	Enhancers	NHEK	skin
9	chr2:40259600-40261400	Enhancers	HSMMtube	muscle
10	chr2:40259600-40261400	Enhancers	NHLF	lung
11	chr2:40259600-40261600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:40259600-40261600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:40259800-40262200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:40260800-40262600	ZNF genes & repeats	Dnd41	blood
15	chr2:40261000-40261400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr2:40261200-40261400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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