Variant report

Variant	rs3847663
Chromosome Location	chr12:60542054-60542055
allele	A/G
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
ENSG00000135655	Chromatin interaction
ENSG00000198673	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10506408	0.87[EUR][1000 genomes]
rs10784027	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10784028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784029	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784033	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877392	0.83[EUR][1000 genomes]
rs10877398	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877399	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10877401	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877402	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877403	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877406	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11173319	0.87[AMR][1000 genomes]
rs11173327	0.84[EUR][1000 genomes]
rs11173328	0.86[EUR][1000 genomes]
rs11173329	0.86[EUR][1000 genomes]
rs11173336	0.86[EUR][1000 genomes]
rs11173338	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11173339	0.87[EUR][1000 genomes]
rs11173340	0.85[EUR][1000 genomes]
rs11173341	0.87[EUR][1000 genomes]
rs11173343	0.87[EUR][1000 genomes]
rs11173345	0.84[EUR][1000 genomes]
rs11173346	0.84[EUR][1000 genomes]
rs11173357	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11173365	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11173371	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11173387	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12230817	0.81[EUR][1000 genomes]
rs12231312	0.84[EUR][1000 genomes]
rs12817959	0.84[AMR][1000 genomes]
rs12830074	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1304313	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1354469	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1389255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1389256	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1493311	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1493318	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1493325	0.83[EUR][1000 genomes]
rs1504444	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1587821	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17595010	0.87[EUR][1000 genomes]
rs17595325	0.93[CEU][hapmap];0.80[GIH][hapmap];0.87[EUR][1000 genomes]
rs17595367	0.87[EUR][1000 genomes]
rs17665306	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs1910674	0.84[AMR][1000 genomes]
rs2014074	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134882	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2172500	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35713358	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3847662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3907482	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4093759	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4254103	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4347425	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4366523	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4406858	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4454757	0.83[EUR][1000 genomes]
rs4491264	0.84[EUR][1000 genomes]
rs4567505	0.84[EUR][1000 genomes]
rs4625509	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4758743	0.84[EUR][1000 genomes]
rs4758744	0.82[EUR][1000 genomes]
rs4758745	0.82[EUR][1000 genomes]
rs4758855	0.92[AMR][1000 genomes]
rs4758858	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61127975	0.80[EUR][1000 genomes]
rs61922949	0.80[EUR][1000 genomes]
rs61922950	0.80[EUR][1000 genomes]
rs61923065	0.87[EUR][1000 genomes]
rs61923066	0.90[EUR][1000 genomes]
rs61923067	0.83[EUR][1000 genomes]
rs61925366	0.84[EUR][1000 genomes]
rs66587505	0.86[EUR][1000 genomes]
rs7134663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7136435	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7138854	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72648145	0.87[EUR][1000 genomes]
rs7297548	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7298315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300532	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302607	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310323	0.82[EUR][1000 genomes]
rs7313364	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7314355	0.82[EUR][1000 genomes]
rs735926	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7961221	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7961816	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7967860	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973156	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7973882	0.83[EUR][1000 genomes]
rs7977065	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7977642	0.80[EUR][1000 genomes]
rs7979069	0.82[EUR][1000 genomes]
rs8181648	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs958543	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9668893	0.82[EUR][1000 genomes]
rs992478	0.89[AMR][1000 genomes];0.83[EUR][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
rs3847663	RDH5	cis	parietal	SCAN

Chromatin state (count:19 , 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	chr12:60540200-60542600	Enhancers	NHDF-Ad	bronchial
3	chr12:60540400-60543400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:60540600-60542400	Enhancers	NHLF	lung
5	chr12:60541200-60542600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr12:60541400-60542400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:60541400-60542800	Enhancers	HMEC	breast
8	chr12:60541400-60542800	Enhancers	HUVEC	blood vessel
9	chr12:60541400-60542800	Enhancers	NHEK	skin
10	chr12:60541400-60543000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:60541600-60542200	Flanking Active TSS	K562	blood
12	chr12:60541600-60542600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:60541600-60542600	Enhancers	Hela-S3	cervix
14	chr12:60541800-60542400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:60541800-60542400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:60541800-60543200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:60542000-60542200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:60542000-60542600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:60542000-60542800	Flanking Active TSS	NH-A	brain

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