Variant report

Variant	rs1517817
Chromosome Location	chr12:83521361-83521362
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10732679	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10735463	0.85[EUR][1000 genomes]
rs1517821	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1517822	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1543170	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1543171	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1796157	1.00[LWK][hapmap]
rs1949427	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2056218	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2292823	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2292827	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3168365	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4882547	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7311514	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv559559	chr12:83505512-83765069	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83516000-83526200	Weak transcription	Fetal Intestine Small	intestine
2	chr12:83516000-83533000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:83516200-83526000	Weak transcription	Gastric	stomach
4	chr12:83516400-83525800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr12:83516400-83526000	Weak transcription	Fetal Stomach	stomach
6	chr12:83516400-83526000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:83516400-83538800	Weak transcription	Fetal Brain Male	brain
8	chr12:83516600-83526000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr12:83516600-83532600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:83516600-83533400	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:83516800-83528600	Weak transcription	Adipose Nuclei	Adipose
12	chr12:83517000-83521800	Weak transcription	Brain Substantia Nigra	brain
13	chr12:83517000-83522200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:83517000-83525800	Weak transcription	Brain Anterior Caudate	brain
15	chr12:83517000-83526200	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:83517200-83526200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:83517200-83528000	Weak transcription	Brain Angular Gyrus	brain
18	chr12:83517200-83528800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:83517400-83526200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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