Variant report

Variant	rs17665306
Chromosome Location	chr12:60542784-60542785
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:60541351..60544237-chr12:60546904..60548454,2	K562	blood:
2	chr12:60540647..60543131-chr12:62652569..62655278,2	K562	blood:

Variant related genes	Relation type
ENSG00000198673	Chromatin interaction
ENSG00000135655	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10506408	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784027	0.83[EUR][1000 genomes]
rs10784028	0.86[EUR][1000 genomes]
rs10877392	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11173327	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11173328	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173329	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173336	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173337	0.80[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11173338	0.85[EUR][1000 genomes]
rs11173339	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173340	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173341	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173343	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173345	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173346	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173351	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11173359	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11173361	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11173367	0.83[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11173386	0.83[ASN][1000 genomes]
rs12226976	0.92[ASN][1000 genomes]
rs12227514	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12228823	0.82[ASN][1000 genomes]
rs12230599	0.81[ASN][1000 genomes]
rs12230817	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12231312	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231943	0.82[ASN][1000 genomes]
rs1319775	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1389255	0.85[EUR][1000 genomes]
rs1493325	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1504442	0.83[ASN][1000 genomes]
rs1504443	0.83[ASN][1000 genomes]
rs17595010	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17595325	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17595367	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17602381	0.96[ASN][1000 genomes]
rs2014074	0.86[EUR][1000 genomes]
rs3847662	0.86[EUR][1000 genomes]
rs3847663	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs3907482	0.84[EUR][1000 genomes]
rs4093759	0.85[EUR][1000 genomes]
rs4143650	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4265627	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4417318	0.86[ASN][1000 genomes]
rs4454757	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4491264	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4567505	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4758743	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4758744	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4758745	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4758859	0.82[ASN][1000 genomes]
rs55661627	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61127975	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61487567	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61922947	0.92[ASN][1000 genomes]
rs61922949	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61922950	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61923065	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61923066	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61923067	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61923074	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61923092	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61923093	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61923121	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61923124	0.83[ASN][1000 genomes]
rs61923127	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61923129	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61923130	0.82[ASN][1000 genomes]
rs61923132	0.82[ASN][1000 genomes]
rs61923156	0.81[ASN][1000 genomes]
rs61923157	0.81[ASN][1000 genomes]
rs61925366	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6581305	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66587505	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7131926	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7134267	0.82[ASN][1000 genomes]
rs7134663	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs7135031	0.93[CEU][hapmap]
rs72648145	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298315	0.85[EUR][1000 genomes]
rs7310323	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7314355	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7957100	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7967860	0.82[EUR][1000 genomes]
rs7973882	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7977065	0.85[EUR][1000 genomes]
rs7977642	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7979069	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8181648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs959645	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9634280	0.83[ASN][1000 genomes]
rs9634281	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9668893	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428591	chr12:60446360-60631044	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv427913	chr12:60462443-60569344	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv2760273	chr12:60489188-60561925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv559108	chr12:60518842-60548334	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1851665	chr12:60522725-60549171	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17665306	RDH5	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60540000-60542800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:60540400-60543400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:60541400-60542800	Enhancers	HMEC	breast
4	chr12:60541400-60542800	Enhancers	HUVEC	blood vessel
5	chr12:60541400-60542800	Enhancers	NHEK	skin
6	chr12:60541400-60543000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:60541800-60543200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:60542000-60542800	Flanking Active TSS	NH-A	brain
9	chr12:60542400-60542800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:60542400-60545800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:60542400-60546200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:60542600-60543000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:60542600-60545000	Weak transcription	NHDF-Ad	bronchial

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