Variant report

Variant	rs12403334
Chromosome Location	chr1:160937964-160937965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1044478	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs1062826	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs1062827	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs11800456	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11800797	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11801591	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11802250	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11802727	1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11802731	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11804166	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11804856	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11807930	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs12403886	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12562121	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12565932	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs17384360	0.88[CHB][hapmap]
rs17388108	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2073655	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs2073656	0.88[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs2247459	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs2247596	0.94[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs2247671	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2247790	0.94[CHB][hapmap];0.81[CHD][hapmap];0.93[JPT][hapmap];0.89[TSI][hapmap]
rs2255852	0.88[JPT][hapmap]
rs2297220	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs2297221	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs2297222	0.82[YRI][hapmap]
rs2481080	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs2481081	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2481084	0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs28544288	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28701476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28726136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28776781	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28809889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35923797	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3737785	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap]
rs3737787	0.88[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs55651159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55688440	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55700711	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55729337	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55890734	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56199992	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56201963	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56289112	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56383095	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61802209	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61802210	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61802214	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61802215	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61802216	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61802217	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61802219	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61802220	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61802221	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61802225	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61802226	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61802227	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61802229	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61802230	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72712826	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72712828	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72712846	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs836	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]
rs869985	1.00[ASW][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12403334	ROBLD3	cis	cerebellum	SCAN
rs12403334	OR10J5	cis	cerebellum	SCAN
rs12403334	ARHGEF11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160931000-160942000	Weak transcription	H9 Cell Line	embryonic stem cell

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