Variant report

Variant	rs12407896
Chromosome Location	chr1:57933955-57933956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10493225	0.85[CHB][hapmap]
rs11207027	0.82[CHB][hapmap]
rs11207041	0.84[EUR][1000 genomes]
rs12044912	0.85[CHB][hapmap]
rs12046102	0.85[CHB][hapmap]
rs12132685	0.85[CHB][hapmap]
rs12726704	0.85[CHB][hapmap]
rs12752978	0.85[CHB][hapmap]
rs1334239	0.85[CHB][hapmap]
rs1334240	0.85[CHB][hapmap]
rs17459948	0.85[CHB][hapmap]
rs2406067	0.84[MEX][hapmap];0.82[EUR][1000 genomes]
rs2781325	0.85[CHB][hapmap]
rs4279875	0.85[CHB][hapmap]
rs6686072	0.84[MEX][hapmap];0.82[EUR][1000 genomes]
rs7519850	0.92[ASN][1000 genomes]
rs7536271	0.81[EUR][1000 genomes]
rs9436130	0.85[CHB][hapmap]

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	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv870908	chr1:57884310-58037783	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12407896	TTC22	cis	cerebellum	SCAN
rs12407896	NFIA	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57930800-57934800	Weak transcription	NHLF	lung
2	chr1:57931000-57934400	Weak transcription	Hela-S3	cervix
3	chr1:57931000-57935200	Weak transcription	Fetal Brain Female	brain
4	chr1:57932800-57942400	Weak transcription	Stomach Mucosa	stomach
5	chr1:57933000-57937000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:57933200-57934800	Enhancers	Fetal Brain Male	brain
7	chr1:57933200-57935800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:57933200-57937000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:57933600-57934000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:57933600-57934000	Enhancers	Psoas Muscle	Psoas
11	chr1:57933600-57934200	Enhancers	Right Atrium	heart
12	chr1:57933600-57937000	Enhancers	NHDF-Ad	bronchial
13	chr1:57933800-57934000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:57933800-57936400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:57933800-57936400	Enhancers	NH-A	brain

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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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