Variant report

Variant	rs1041238
Chromosome Location	chr1:166974420-166974421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IKZF1	chr1:166974363-166974456	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNA5SP65	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10918603	0.84[CHD][hapmap]
rs10918607	0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10918608	0.97[ASN][1000 genomes]
rs11578336	0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs11802666	0.94[ASN][1000 genomes]
rs11805946	0.95[ASN][1000 genomes]
rs12118335	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126991	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12131832	1.00[ASN][1000 genomes]
rs12133327	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12134016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12145919	0.93[ASN][1000 genomes]
rs12564877	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12569084	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2296837	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2312487	0.98[ASN][1000 genomes]
rs2312675	0.80[CHB][hapmap]
rs3736988	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs41269702	0.85[ASN][1000 genomes]
rs56093705	0.96[ASN][1000 genomes]
rs61447801	0.95[ASN][1000 genomes]
rs61606407	0.85[ASN][1000 genomes]
rs6427053	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs6655947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6660048	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6662130	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665341	0.85[ASN][1000 genomes]
rs6669886	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs6673622	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6673720	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6677644	0.84[CHD][hapmap]
rs6681562	1.00[ASN][1000 genomes]
rs6681571	0.99[ASN][1000 genomes]
rs6682062	0.85[ASN][1000 genomes]
rs6695162	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6695609	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6696203	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs6697417	0.86[ASN][1000 genomes]
rs6699159	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7511933	0.95[ASN][1000 genomes]
rs7518155	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs7520897	0.84[CHD][hapmap]
rs7528849	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs7533688	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7545806	0.84[CHD][hapmap]
rs7545911	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7550698	0.85[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	nsv1004148	chr1:166951869-167016311	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2750815	chr1:166953866-167180342	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1041238	TIPRL	cis	cerebellum	SCAN
rs1041238	FAM78B	cis	parietal	SCAN
rs1041238	C1orf192	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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