Variant report

Variant	rs28969986
Chromosome Location	chr2:234552407-234552408
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	2:234543708-234558325..2:234772667-234780240	Hela-S3	cervix:
2	2:234543708-234558325..2:234649753-234657866	Hela-S3	cervix:
3	2:234492023-234494396..2:234543708-234558325	GM12878	blood:

Variant related genes	Relation type
ENSG00000227802	Chromatin interaction
ENSG00000224287	Chromatin interaction
ENSG00000228949	Chromatin interaction
ENSG00000228445	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1597942	1.00[YRI][hapmap]
rs28898576	1.00[AMR][1000 genomes]
rs28898577	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs28948380	1.00[AFR][1000 genomes]
rs28966994	1.00[YRI][hapmap]
rs28968511	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28968512	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs28968514	1.00[AFR][1000 genomes]
rs28969672	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28969674	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28969678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28969696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28969700	1.00[YRI][hapmap]
rs28969989	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28969990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28969996	1.00[AMR][1000 genomes]
rs28970001	1.00[AMR][1000 genomes]
rs28970002	1.00[AMR][1000 genomes]
rs28970009	1.00[AMR][1000 genomes]
rs28970016	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv3445986	chr2:234494952-234557707	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	esv3419326	chr2:234498411-234560470	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
6	esv2762307	chr2:234504523-234561979	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
7	nsv1007561	chr2:234507291-234560670	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
8	nsv536181	chr2:234507291-234560670	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
9	esv3406377	chr2:234517448-234558127	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	nsv876015	chr2:234518011-234579915	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
11	nsv961572	chr2:234526394-234559587	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	nsv584704	chr2:234526680-234569137	Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
13	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234547800-234554000	Weak transcription	Colonic Mucosa	Colon
2	chr2:234551600-234553800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:234551800-234559200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:234552400-234552600	Enhancers	Esophagus	oesophagus

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