Variant report

Variant	rs2304053
Chromosome Location	chr5:150942969-150942970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:150942025..150944523-chr5:150961662..150964571,2	K562	blood:
2	chr5:150933953..150936226-chr5:150941566..150943074,2	K562	blood:
3	chr5:150933361..150936096-chr5:150939863..150943066,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10044120	0.83[CHB][hapmap]
rs10052817	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054406	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10060613	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10060662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10069540	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10069901	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10072841	0.83[CHB][hapmap]
rs10085060	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12055366	1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs13158643	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13159039	0.81[CEU][hapmap]
rs1432862	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1541910	0.89[ASN][1000 genomes]
rs2163769	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2304054	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28449749	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34335300	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34346367	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35908499	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35957412	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3734055	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3734057	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3734058	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3734059	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3734060	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4320248	0.94[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6859217	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6878528	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6878532	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6878556	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6878627	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6879740	0.86[ASN][1000 genomes]
rs6883153	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6883216	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6890712	0.87[MKK][hapmap];0.92[YRI][hapmap]
rs7724472	0.90[ASN][1000 genomes]
rs7726769	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7727173	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7737011	0.94[CHB][hapmap]
rs7737419	0.87[CHB][hapmap]
rs9324698	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9324699	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9324700	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][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	esv20633	chr5:150941705-150955343	Strong transcription Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2304053	JAKMIP2	cis	cerebellum	SCAN
rs2304053	PPARGC1B	cis	cerebellum	SCAN
rs2304053	PCYOX1L	cis	parietal	SCAN
rs2304053	CNOT8	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:150908200-150948000	Strong transcription	HMEC	breast
2	chr5:150908400-150944000	Strong transcription	NHEK	skin
3	chr5:150918200-150945400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:150934200-150949600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:150937000-150948600	Weak transcription	Right Atrium	heart
6	chr5:150937600-150948600	Weak transcription	Adipose Nuclei	Adipose
7	chr5:150940800-150943200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:150942400-150943400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:150942600-150948400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:150942800-150944000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:150942800-150945000	Weak transcription	Esophagus	oesophagus

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