Variant report

Variant	rs227114
Chromosome Location	chr1:70124742-70124743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:129)

rs_ID	r²[population]
rs1065629	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs1145922	1.00[JPT][hapmap]
rs1145923	0.89[EUR][1000 genomes]
rs1145924	1.00[JPT][hapmap]
rs1154974	0.88[EUR][1000 genomes]
rs1245039	1.00[JPT][hapmap]
rs1245040	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1245043	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1245045	0.85[EUR][1000 genomes]
rs1245046	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1245047	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs1245049	0.94[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs1245050	0.85[EUR][1000 genomes]
rs1245051	0.85[EUR][1000 genomes]
rs1245052	0.86[EUR][1000 genomes]
rs1245053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1245054	0.93[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs1245056	0.85[EUR][1000 genomes]
rs1245057	0.84[EUR][1000 genomes]
rs1245058	0.94[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs1245061	0.84[EUR][1000 genomes]
rs1245063	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1245067	0.85[EUR][1000 genomes]
rs1245068	0.81[EUR][1000 genomes]
rs1245069	0.81[EUR][1000 genomes]
rs1245070	0.83[CEU][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs1245072	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1261871	0.85[EUR][1000 genomes]
rs1264402	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1264407	1.00[JPT][hapmap]
rs1264408	1.00[JPT][hapmap]
rs1264409	1.00[JPT][hapmap]
rs1264413	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1270432	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1270434	0.85[EUR][1000 genomes]
rs1270435	0.87[EUR][1000 genomes]
rs1271928	0.94[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs1341778	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs1341779	0.85[EUR][1000 genomes]
rs1341780	0.85[EUR][1000 genomes]
rs1341781	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1361613	0.94[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs1418007	0.85[EUR][1000 genomes]
rs1418008	0.85[EUR][1000 genomes]
rs1418012	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs1615332	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1618786	0.87[EUR][1000 genomes]
rs1619463	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1622158	0.85[EUR][1000 genomes]
rs1622893	0.85[EUR][1000 genomes]
rs1623673	0.94[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs1625490	0.85[EUR][1000 genomes]
rs1627769	0.85[EUR][1000 genomes]
rs1628716	0.84[EUR][1000 genomes]
rs1631834	0.94[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs17324599	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17396516	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1749459	0.94[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs1749473	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1749484	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs1749492	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1749494	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1749496	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1749497	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1749498	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1749499	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1749500	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1749502	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1749504	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1749506	0.85[EUR][1000 genomes]
rs1749507	0.94[CEU][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs1749508	0.85[EUR][1000 genomes]
rs1749510	0.87[EUR][1000 genomes]
rs1749512	0.85[EUR][1000 genomes]
rs1749514	0.85[EUR][1000 genomes]
rs1749515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1749517	0.94[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs1749520	0.85[EUR][1000 genomes]
rs1773309	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1773313	0.85[EUR][1000 genomes]
rs1773314	0.85[EUR][1000 genomes]
rs1773315	0.85[EUR][1000 genomes]
rs1773316	0.85[EUR][1000 genomes]
rs1773317	0.85[EUR][1000 genomes]
rs1773318	0.85[EUR][1000 genomes]
rs1773319	0.87[EUR][1000 genomes]
rs1773320	0.85[EUR][1000 genomes]
rs1773321	0.94[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs1773322	0.85[EUR][1000 genomes]
rs1773324	0.85[EUR][1000 genomes]
rs1773325	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs1773327	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs1773329	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1773330	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1773332	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1773333	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1773335	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs1773336	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1773337	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1773338	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1773339	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1773340	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1773344	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs1773346	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1773348	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1773350	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2094037	0.81[EUR][1000 genomes]
rs2094039	0.82[ASN][1000 genomes]
rs2104407	0.80[EUR][1000 genomes]
rs2147785	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2209456	0.85[EUR][1000 genomes]
rs227097	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227100	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227102	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs227104	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs227105	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs227107	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs227113	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2487762	0.85[EUR][1000 genomes]
rs2487763	0.85[EUR][1000 genomes]
rs2487764	0.85[EUR][1000 genomes]
rs2764530	0.94[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs2764532	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2764534	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2764535	0.84[EUR][1000 genomes]
rs966069	0.85[EUR][1000 genomes]
rs966070	0.85[EUR][1000 genomes]
rs966071	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949691	chr1:69749722-70302201	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3384194	chr1:69885024-70275430	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830126	chr1:70014879-70167979	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2764189	chr1:70111889-70137513	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs227114	RPE65	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70106200-70126000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr1:70112400-70126000	Weak transcription	Brain Anterior Caudate	brain
3	chr1:70122600-70126000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:70122800-70124800	Weak transcription	Brain Hippocampus Middle	brain
5	chr1:70123400-70125200	Enhancers	Primary T cells from cord blood	blood
6	chr1:70124000-70124800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:70124600-70124800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:70124600-70126800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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