Variant report

Variant	rs7040414
Chromosome Location	chr9:104059627-104059628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1341770	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361611	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1361612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1418001	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1418002	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59812628	1.00[EUR][1000 genomes]
rs61744526	1.00[EUR][1000 genomes]
rs7021563	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7030643	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7033464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7033605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7036576	1.00[CEU][hapmap]
rs7044194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7864689	1.00[EUR][1000 genomes]
rs7864791	1.00[EUR][1000 genomes]
rs7867050	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7874930	1.00[EUR][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	nsv1037157	chr9:104045761-104149233	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1049740	chr9:104049624-104075825	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7040414	ZNF12	trans	lymphoblastoid	RTeQTL
rs7040414	TNFRSF17	trans	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104046000-104061800	Weak transcription	Brain Substantia Nigra	brain
2	chr9:104048800-104071600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr9:104051400-104067800	Weak transcription	HepG2	liver
4	chr9:104059200-104060000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr9:104059400-104059800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr9:104059400-104059800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:104059600-104059800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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Input of quick search could be:

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

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