Variant report

Variant	rs12328637
Chromosome Location	chr2:86824181-86824182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1015117	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs10169746	0.84[ASN][1000 genomes]
rs10180036	0.92[CEU][hapmap];0.85[YRI][hapmap]
rs10184584	0.83[ASN][1000 genomes]
rs10184879	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10187753	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10187880	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1020306	0.81[EUR][1000 genomes]
rs10432704	0.82[ASN][1000 genomes]
rs1080551	0.84[ASN][1000 genomes]
rs11127045	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11127046	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11127047	0.90[CHB][hapmap];0.81[GIH][hapmap];0.83[ASN][1000 genomes]
rs1137684	0.82[EUR][1000 genomes]
rs11676576	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11684230	0.82[EUR][1000 genomes]
rs11689330	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12613282	0.96[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12614447	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12615285	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12623509	0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12714186	0.96[CEU][hapmap];0.83[GIH][hapmap];0.80[LWK][hapmap];0.93[TSI][hapmap]
rs12714188	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12714190	0.97[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap]
rs12714198	0.86[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs12714199	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs12987172	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12991654	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13015620	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13034615	0.86[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13390713	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13408041	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13429696	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1518807	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs1629293	0.97[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap]
rs2241803	1.00[ASW][hapmap];0.96[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2292887	1.00[ASW][hapmap];0.96[CEU][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs308900	0.97[ASN][1000 genomes]
rs308902	0.91[GIH][hapmap]
rs308903	0.89[GIH][hapmap]
rs308910	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs308914	0.95[GIH][hapmap];0.86[MKK][hapmap];0.80[TSI][hapmap]
rs308915	0.87[GIH][hapmap]
rs3201448	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs34666164	0.84[ASN][1000 genomes]
rs3731812	0.82[EUR][1000 genomes]
rs3755002	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs422240	0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];0.96[ASN][1000 genomes]
rs4832040	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832041	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4832043	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4832045	0.82[ASN][1000 genomes]
rs4832297	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832299	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4832300	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832302	0.84[ASN][1000 genomes]
rs4832303	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4832304	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62147239	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6728211	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6733569	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6738663	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6750226	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6752371	0.97[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.82[ASN][1000 genomes]
rs689912	0.84[ASN][1000 genomes]
rs7369138	0.82[EUR][1000 genomes]
rs7557796	0.81[GIH][hapmap]
rs7570640	0.84[ASN][1000 genomes]
rs7584882	0.97[CHD][hapmap];0.91[GIH][hapmap];0.82[ASN][1000 genomes]
rs7587034	0.84[ASN][1000 genomes]
rs7596717	0.97[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs7601115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284788	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs958561	0.86[ASW][hapmap];0.96[CEU][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1011590	chr2:86824181-86906114	Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12328637	VPS24	cis	lymphoblastoid	seeQTL
rs12328637	POLR1A	cis	parietal	SCAN
rs12328637	POLR1A	cis	cerebellum	SCAN
rs12328637	RNF103	cis	cerebellum	SCAN
rs12328637	C2orf68	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86819800-86831000	Weak transcription	Fetal Brain Female	brain
2	chr2:86820000-86830600	Weak transcription	Brain Anterior Caudate	brain
3	chr2:86820000-86830800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:86820200-86831000	Weak transcription	Fetal Brain Male	brain
5	chr2:86820200-86831000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:86820400-86828400	Weak transcription	Fetal Stomach	stomach
7	chr2:86820600-86831000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:86822200-86824200	Enhancers	Rectal Smooth Muscle	rectum
9	chr2:86823000-86830600	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:86823200-86842800	Weak transcription	Psoas Muscle	Psoas
11	chr2:86823400-86826200	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:86823600-86831200	Weak transcription	HSMMtube	muscle
13	chr2:86823800-86824200	Flanking Active TSS	Fetal Heart	heart
14	chr2:86824000-86830800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:86824000-86831000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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