Variant report

Variant	rs4931166
Chromosome Location	chr12:29356263-29356264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10492385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10771493	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11050088	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11050117	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11050120	0.91[JPT][hapmap]
rs11050124	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11050132	0.92[EUR][1000 genomes]
rs11830434	0.91[LWK][hapmap];0.94[YRI][hapmap]
rs12371983	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2196488	0.92[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4414260	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4931157	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6487782	0.85[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296314	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7301408	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7302742	0.89[CEU][hapmap];0.87[GIH][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs7969731	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4931166	IFLTD1	cis	parietal	SCAN
rs4931166	SSPN	cis	parietal	SCAN
rs4931166	FGFR1OP2	cis	parietal	SCAN
rs4931166	ZNF561	trans	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29325400-29364600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:29346000-29360800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:29354000-29360400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:29354200-29357600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:29355800-29357000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:29355800-29357200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:29355800-29357600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:29355800-29359000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:29356000-29356600	Strong transcription	Monocytes-CD14+_RO01746	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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