Variant report

Variant	rs7679010
Chromosome Location	chr4:48083885-48083886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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];0.82[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];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13123671	0.95[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	0.94[AFR][1000 genomes];0.98[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];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1567218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[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];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34059656	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35067106	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35201668	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35494193	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35590286	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792624	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4589663	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]
rs4695330	0.93[CHD][hapmap]
rs55718430	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67723804	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6825925	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6844940	0.82[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];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73244480	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654844	0.82[AFR][1000 genomes];0.95[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]

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
rs7679010	TXK	cis	parietal	SCAN

Chromatin state (count:32 , 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	chr4:48069800-48088000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr4:48070800-48105200	Weak transcription	GM12878-XiMat	blood
4	chr4:48073800-48088000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:48073800-48088000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:48076600-48092400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:48079000-48084600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:48079000-48087400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr4:48080600-48084600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:48080600-48084600	Enhancers	Hela-S3	cervix
11	chr4:48080600-48085200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr4:48081600-48094200	Weak transcription	Pancreas	Pancrea
13	chr4:48082400-48085200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:48082400-48088400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:48082600-48084000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:48082600-48084000	Enhancers	NH-A	brain
17	chr4:48082600-48084400	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr4:48082600-48085200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:48082600-48086200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr4:48082600-48088000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:48082800-48084400	Enhancers	HUVEC	blood vessel
22	chr4:48082800-48088200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:48082800-48088200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:48083000-48098000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:48083000-48098200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:48083400-48084000	Enhancers	A549	lung
27	chr4:48083400-48084200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:48083400-48098200	Strong transcription	Primary T cells from cord blood	blood
29	chr4:48083800-48084000	Enhancers	Placenta	Placenta
30	chr4:48083800-48084400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr4:48083800-48084400	Enhancers	HSMM	muscle
32	chr4:48083800-48084600	Genic enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links