Variant report

Variant	rs16858244
Chromosome Location	chr2:12228679-12228680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11680545	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12993594	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13021784	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1344933	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34253770	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34970030	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6729317	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72610740	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv999704	chr2:12153766-12243960	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1005069	chr2:12161023-12242734	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1000696	chr2:12162843-12241022	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv997538	chr2:12216408-12242734	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr2:12217400-12249800	Weak transcription	GM12878-XiMat	blood
2	chr2:12221000-12234200	Weak transcription	Spleen	Spleen
3	chr2:12224400-12230800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:12224600-12236400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:12224800-12229600	Weak transcription	Brain Germinal Matrix	brain
6	chr2:12224800-12238000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:12227200-12229200	Enhancers	NHEK	skin
8	chr2:12227200-12229400	Enhancers	HMEC	breast
9	chr2:12227400-12229000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:12227400-12229000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:12227400-12229200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:12227400-12230000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:12227800-12228800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:12227800-12229400	Enhancers	NHDF-Ad	bronchial
15	chr2:12228000-12229200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:12228200-12230800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:12228400-12236400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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dbSNP/dbVar ID: rs12345 /nsv7879
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