Variant report

Variant	rs16949897
Chromosome Location	chr12:120481140-120481141
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10492050	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12301083	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16949828	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16949884	1.00[ASW][hapmap];1.00[LWK][hapmap];0.89[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]
rs16949890	1.00[ASW][hapmap];1.00[LWK][hapmap];0.89[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]
rs35938105	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3852590	1.00[EUR][1000 genomes]
rs56792569	1.00[EUR][1000 genomes]
rs59159546	1.00[EUR][1000 genomes]
rs61733796	1.00[EUR][1000 genomes]
rs61753910	1.00[EUR][1000 genomes]
rs7953006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16949897	CD4	trans	lymphoblastoid	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120454200-120484800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:120479200-120481200	Enhancers	HMEC	breast
3	chr12:120479200-120481400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:120479200-120481600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:120479200-120481600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:120479600-120481600	Enhancers	HepG2	liver
7	chr12:120479800-120485000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:120480000-120481200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:120480000-120499200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr12:120480000-120499200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:120480200-120481400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:120480200-120481400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:120480200-120481600	Enhancers	NHEK	skin
14	chr12:120480200-120484400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:120480200-120484800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:120480200-120485000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:120480200-120485400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:120480800-120482200	Enhancers	Stomach Mucosa	stomach
19	chr12:120480800-120485200	Weak transcription	Primary T cells from cord blood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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