Variant report

Variant	rs28901629
Chromosome Location	chr2:234851094-234851095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	2:234683624-234705119..2:234843685-234852750	Hela-S3	cervix:
2	2:234543708-234558325..2:234843685-234852750	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000242515	Chromatin interaction
ENSG00000234143	Chromatin interaction
ENSG00000185038	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11562977	0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes]
rs11563214	0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs11563218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs12617866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12620352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1468521	1.00[EUR][1000 genomes]
rs2362291	0.93[CHB][hapmap];0.83[JPT][hapmap];1.00[EUR][1000 genomes]
rs28901579	1.00[EUR][1000 genomes]
rs28901582	1.00[EUR][1000 genomes]
rs28901591	0.93[CHB][hapmap];0.83[JPT][hapmap];1.00[EUR][1000 genomes]
rs28901600	1.00[EUR][1000 genomes]
rs28901608	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs28901610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28901615	1.00[EUR][1000 genomes]
rs28901618	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28901637	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28901868	0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs28902174	0.83[EUR][1000 genomes]
rs4663342	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4663343	0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs4663989	1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7602303	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs9789366	0.93[CHB][hapmap];0.91[JPT][hapmap];1.00[EUR][1000 genomes]
rs9789398	0.93[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes]
rs9789675	0.93[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv876024	chr2:234842650-234856421	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234845400-234851400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:234848000-234851600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:234848000-234852800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:234849400-234883400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:234849600-234873800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:234851000-234851600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:234851000-234851600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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