Variant report

Variant	rs293844
Chromosome Location	chr3:191131946-191131947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10937477	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs1347400	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1465737	0.84[EUR][1000 genomes]
rs1473866	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs150506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159488	0.87[ASN][1000 genomes]
rs159489	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176820	0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs186063	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap]
rs186066	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188384	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs188385	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs192671	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs293797	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.91[ASN][1000 genomes]
rs293798	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs293800	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293802	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293804	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293805	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs293806	0.82[CHB][hapmap];0.95[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293808	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293809	0.89[TSI][hapmap]
rs293810	0.89[TSI][hapmap]
rs293811	0.89[TSI][hapmap]
rs293813	0.89[TSI][hapmap]
rs293815	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs293840	0.89[TSI][hapmap]
rs293846	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293851	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297396	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs364519	0.89[TSI][hapmap]
rs366626	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs367747	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368665	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs369174	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381090	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383075	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs389765	0.89[TSI][hapmap]
rs390744	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401465	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs420266	0.89[TSI][hapmap]
rs426466	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429374	0.89[TSI][hapmap]
rs432085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434556	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs436393	0.89[TSI][hapmap]
rs437244	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs438589	0.89[TSI][hapmap]
rs448133	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs448643	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4677630	1.00[ASW][hapmap];0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4677734	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs4677735	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs523270	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs525774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529523	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566548	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6779820	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs6953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697905	0.82[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs709142	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847278	0.85[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	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs293844	CCDC50	cis	Artery Tibial	GTEx
rs293844	UTS2D	cis	parietal	SCAN
rs293844	TFRC	cis	parietal	SCAN
rs293844	PIGX	cis	cerebellum	SCAN
rs293844	CCDC50	cis	Thyroid	GTEx
rs293844	CCDC50	cis	Artery Aorta	GTEx
rs293844	PPP1R2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191129000-191134600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:191129400-191135200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:191130200-191132800	Enhancers	NHDF-Ad	bronchial
4	chr3:191130400-191132200	Enhancers	HSMMtube	muscle
5	chr3:191130600-191132800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:191130800-191132000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:191130800-191132200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:191131000-191132000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:191131000-191132000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:191131000-191132000	Weak transcription	HSMM	muscle
11	chr3:191131000-191132000	Weak transcription	Osteobl	bone
12	chr3:191131000-191132200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:191131800-191132200	Enhancers	NHEK	skin
14	chr3:191131800-191132400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:191131800-191132600	Enhancers	NHLF	lung

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