Variant report

Variant	rs2013289
Chromosome Location	chr6:5593550-5593551
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1985346	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2064109	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2142736	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2326648	0.88[EUR][1000 genomes]
rs2326649	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[EUR][1000 genomes]
rs2326651	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4960102	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs4960106	0.93[CEU][hapmap]
rs4960107	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4960108	0.83[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5012511	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6597144	0.93[EUR][1000 genomes]
rs6597147	0.93[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6903542	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6941763	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7738509	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs7739718	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7744153	0.89[ASW][hapmap];0.88[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7744367	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7744837	1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs7765047	0.88[CEU][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7765256	0.83[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9328318	0.89[ASW][hapmap];0.88[CEU][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9328319	0.89[ASW][hapmap];0.88[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9328320	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9392084	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9392698	0.86[CHD][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs9405276	0.87[CEU][hapmap];0.84[CHB][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9405852	0.94[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs9405853	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9502320	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1016905	chr6:5566364-5639167	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv970722	chr6:5588680-5593976	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2013289	KRTAP24-1	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5577400-5639800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5581000-5614200	Weak transcription	Lung	lung
3	chr6:5581000-5640400	Weak transcription	Gastric	stomach
4	chr6:5582200-5595000	Weak transcription	Fetal Stomach	stomach
5	chr6:5587000-5595200	Weak transcription	Spleen	Spleen
6	chr6:5587200-5619400	Weak transcription	Primary B cells from cord blood	blood
7	chr6:5589600-5594000	Weak transcription	Esophagus	oesophagus
8	chr6:5590000-5604400	Weak transcription	Pancreas	Pancrea
9	chr6:5590800-5622000	Weak transcription	Right Atrium	heart
10	chr6:5591000-5595600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:5591200-5619000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:5591600-5626400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:5591800-5597200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:5591800-5605000	Weak transcription	Primary T cells from cord blood	blood
15	chr6:5592200-5619200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:5593000-5593600	Flanking Active TSS	K562	blood
17	chr6:5593000-5594400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:5593200-5593600	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr6:5593200-5604200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:5593400-5621000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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