Variant report

Variant	rs6873241
Chromosome Location	chr5:35890002-35890003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10058723	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10064778	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065462	1.00[ASN][1000 genomes]
rs10078972	1.00[ASN][1000 genomes]
rs10079517	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11567693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11567757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739191	1.00[ASN][1000 genomes]
rs11951270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11953540	1.00[TSI][hapmap]
rs11953960	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11954524	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11958548	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11959495	1.00[EUR][1000 genomes]
rs11960054	1.00[EUR][1000 genomes]
rs16902710	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1874182	1.00[EUR][1000 genomes]
rs1965840	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2172777	1.00[EUR][1000 genomes]
rs2277042	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2277044	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4022390	1.00[EUR][1000 genomes]
rs4346794	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4361544	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4361545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6451224	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6451255	1.00[EUR][1000 genomes]
rs6860528	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6860903	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862072	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875303	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6880287	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881747	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6889625	1.00[ASN][1000 genomes]
rs6890572	1.00[ASN][1000 genomes]
rs6896114	1.00[EUR][1000 genomes]
rs6896401	1.00[EUR][1000 genomes]
rs6896576	1.00[EUR][1000 genomes]
rs73748793	1.00[EUR][1000 genomes]
rs766065	1.00[EUR][1000 genomes]
rs7700501	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7700688	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7702340	1.00[EUR][1000 genomes]
rs7703463	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7705125	1.00[EUR][1000 genomes]
rs7710047	1.00[EUR][1000 genomes]
rs7719226	1.00[EUR][1000 genomes]
rs7723314	1.00[EUR][1000 genomes]
rs7730148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7733484	1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830261	chr5:35863084-36018048	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6873241	AHSP	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35885200-35890600	Weak transcription	NHEK	skin
2	chr5:35885400-35890400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:35885600-35890600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:35888400-35890400	Weak transcription	Dnd41	blood
5	chr5:35889000-35890200	Weak transcription	Placenta	Placenta
6	chr5:35889200-35891000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:35889400-35890400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:35889800-35891400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:35890000-35890400	Weak transcription	Fetal Thymus	thymus
10	chr5:35890000-35890400	Weak transcription	NHLF	lung
11	chr5:35890000-35890800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr5:35890000-35891200	Enhancers	Thymus	Thymus

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