Variant report

Variant	rs12616060
Chromosome Location	chr2:99487972-99487973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12232948	1.00[CHB][hapmap]
rs12611969	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]
rs12612736	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12614153	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615518	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616866	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12617554	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12619244	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12620812	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12622254	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12622445	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12623022	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623171	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623172	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623472	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021968	1.00[MEX][hapmap]
rs17022063	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2871242	0.86[AMR][1000 genomes]
rs35979410	1.00[CHB][hapmap];0.90[AMR][1000 genomes]
rs4851165	0.87[GIH][hapmap]
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];0.83[ASN][1000 genomes]
rs72958631	0.86[AMR][1000 genomes]
rs7557719	0.83[AMR][1000 genomes]
rs868921	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99484000-99489000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:99485000-99488200	Enhancers	Fetal Muscle Leg	muscle
3	chr2:99485600-99499800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:99485800-99488200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:99485800-99491800	Weak transcription	Brain Anterior Caudate	brain
6	chr2:99486000-99488600	Weak transcription	Right Atrium	heart
7	chr2:99486200-99489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:99486400-99488000	Enhancers	Esophagus	oesophagus
9	chr2:99486400-99489600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:99486600-99489400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:99486600-99489800	Weak transcription	NHEK	skin
12	chr2:99486800-99489600	Weak transcription	Placenta	Placenta
13	chr2:99486800-99491000	Weak transcription	GM12878-XiMat	blood
14	chr2:99487000-99489600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:99487000-99489600	Weak transcription	HMEC	breast
16	chr2:99487600-99499400	Weak transcription	Gastric	stomach
17	chr2:99487800-99489000	Enhancers	Pancreatic Islets	Pancreatic Islet

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