Variant report

Variant	rs12611969
Chromosome Location	chr2:99478968-99478969
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	chr2:99223225..99225395-chr2:99478487..99481431,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115446	Chromatin interaction
ENSG00000183513	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12232948	1.00[CHB][hapmap]
rs12612736	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614153	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12615518	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12616060	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616866	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12617554	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12619244	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12620812	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12622254	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622445	1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12623022	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623171	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623172	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623472	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17022063	1.00[YRI][hapmap]
rs2871242	0.86[AMR][1000 genomes]
rs35979410	1.00[CHB][hapmap];0.90[AMR][1000 genomes]
rs56943554	0.90[AMR][1000 genomes]
rs57480100	0.90[AMR][1000 genomes]
rs61419135	0.90[AMR][1000 genomes]
rs61552487	0.90[AMR][1000 genomes]
rs61604726	0.90[AMR][1000 genomes]
rs6760422	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs72958631	0.86[AMR][1000 genomes]
rs7557719	0.83[AMR][1000 genomes]
rs868921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99463400-99485400	Weak transcription	Gastric	stomach
2	chr2:99478200-99480000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:99478600-99481600	Weak transcription	Aorta	Aorta
4	chr2:99478600-99484600	Weak transcription	Esophagus	oesophagus
5	chr2:99478600-99485400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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