Variant report

Variant	rs1466998
Chromosome Location	chr4:48097400-48097401
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10007288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13123671	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133062	0.89[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs13138066	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13148174	0.83[ASN][1000 genomes]
rs1567218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17674224	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34059656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35067106	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35201668	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35494193	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35590286	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4589663	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695330	0.86[CHD][hapmap]
rs55718430	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60251898	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs67723804	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6825925	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6844940	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6850108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73244480	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7654844	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7658300	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs7679010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1466998	TXK	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48067600-48102400	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr4:48070800-48105200	Weak transcription	GM12878-XiMat	blood
3	chr4:48083000-48098000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:48083000-48098200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr4:48083400-48098200	Strong transcription	Primary T cells from cord blood	blood
6	chr4:48084400-48098000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr4:48084600-48101600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:48085200-48102400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr4:48086400-48099000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:48088600-48104000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:48088600-48106000	Weak transcription	Fetal Thymus	thymus
12	chr4:48088600-48107800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:48088800-48105200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:48090000-48100800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:48090800-48098600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
16	chr4:48091600-48101000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:48092400-48098200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:48092600-48098400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:48092800-48098200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:48096600-48097800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:48096600-48097800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:48096800-48105000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:48097200-48105000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:48097200-48105400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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