Variant report

Variant	rs6829490
Chromosome Location	chr4:48067867-48067868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10517204	0.83[JPT][hapmap]
rs10805163	0.83[JPT][hapmap]
rs12511511	0.97[ASN][1000 genomes]
rs13107767	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1396051	0.83[JPT][hapmap]
rs1507925	0.97[ASN][1000 genomes]
rs2230594	0.99[ASN][1000 genomes]
rs28650378	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28667740	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33964061	0.99[ASN][1000 genomes]
rs3805187	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4340770	0.81[ASN][1000 genomes]
rs4694880	0.83[JPT][hapmap]
rs4695332	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6447610	0.94[ASN][1000 genomes]
rs6447611	0.94[ASN][1000 genomes]
rs6447612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447614	0.99[ASN][1000 genomes]
rs6839501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs906487	0.80[ASN][1000 genomes]
rs9996535	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6829490	TXK	cis	parietal	SCAN
rs6829490	TEC	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48061200-48075200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr4:48061400-48068200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:48061600-48068600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr4:48061800-48068400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:48064600-48068800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:48065400-48068600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:48065400-48069600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr4:48066400-48068200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr4:48066800-48076400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:48067000-48082000	Strong transcription	Primary T cells from cord blood	blood
11	chr4:48067400-48078600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:48067600-48069200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr4:48067600-48069800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:48067600-48073200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:48067600-48080400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr4:48067600-48081200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:48067600-48102400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:48067800-48068800	Enhancers	GM12878-XiMat	blood
19	chr4:48067800-48075200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:48067800-48081600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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