Variant report

Variant	rs16828558
Chromosome Location	chr2:149087825-149087826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10206881	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10469577	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11677584	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11683055	0.90[EUR][1000 genomes]
rs12463708	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12466076	0.85[AMR][1000 genomes]
rs12473137	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12474154	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13386157	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13388448	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13390004	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13410839	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13411082	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427917	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13432173	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16828491	0.91[GIH][hapmap]
rs16828564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17355354	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28773905	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4563168	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56178042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61304079	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6430309	0.82[EUR][1000 genomes]
rs6724259	0.82[EUR][1000 genomes]
rs7590235	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7590487	0.83[AMR][1000 genomes];0.82[EUR][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	nsv1009608	chr2:148897348-149133718	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2753542	chr2:149004714-149268503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1012275	chr2:149031668-149316793	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv523090	chr2:149037012-149110873	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1012123	chr2:149078500-149151358	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149012800-149096000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:149059400-149100400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:149061200-149095800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:149067200-149095800	Weak transcription	HSMM	muscle
5	chr2:149069200-149096400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:149069400-149096000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:149069400-149100200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:149071000-149105000	Weak transcription	Thymus	Thymus
9	chr2:149071400-149100400	Weak transcription	Ovary	ovary
10	chr2:149071600-149094000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:149071800-149095800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:149071800-149100400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:149075600-149093600	Weak transcription	Primary T cells from cord blood	blood
14	chr2:149079800-149093600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:149079800-149094000	Weak transcription	Left Ventricle	heart
16	chr2:149085400-149100400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr2:149086400-149099600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:149086400-149099800	Weak transcription	GM12878-XiMat	blood
19	chr2:149086600-149093600	Weak transcription	Primary B cells from cord blood	blood
20	chr2:149086800-149094000	Weak transcription	Dnd41	blood
21	chr2:149086800-149098200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:149086800-149100400	Weak transcription	Primary B cells from peripheral blood	blood

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