Variant report

Variant	rs4589663
Chromosome Location	chr4:48080573-48080574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48072329..48074417-chr4:48078865..48081474,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10007288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13118073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13123671	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13133062	0.89[ASW][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs13138066	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1466998	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]
rs1567218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17674224	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34059656	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35067106	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35201668	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35494193	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35590286	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792624	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4695330	0.93[CHD][hapmap]
rs55718430	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67723804	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6825925	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6844940	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6850108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244480	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654844	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7658300	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs7679010	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];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs4589663	TXK	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48067000-48082000	Strong transcription	Primary T cells from cord blood	blood
2	chr4:48067600-48081200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:48067600-48102400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr4:48067800-48081600	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr4:48069600-48082600	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr4:48069800-48088000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:48070800-48105200	Weak transcription	GM12878-XiMat	blood
8	chr4:48073800-48088000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:48073800-48088000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr4:48074000-48080600	Weak transcription	Hela-S3	cervix
11	chr4:48075800-48082000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr4:48076000-48081400	Weak transcription	HMEC	breast
13	chr4:48076200-48080600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:48076400-48081800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:48076600-48082200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:48076600-48092400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr4:48076800-48081600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:48077200-48080800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:48077200-48082000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:48077400-48082000	Weak transcription	Stomach Mucosa	stomach
21	chr4:48079000-48084600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:48079000-48087400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr4:48080000-48080600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:48080000-48082000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr4:48080200-48081800	Enhancers	Placenta	Placenta
26	chr4:48080400-48081600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links