Variant report

Variant	rs642652
Chromosome Location	chr2:72622480-72622481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 195 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:188)

rs_ID	r²[population]
rs10168145	1.00[CHB][hapmap]
rs10173381	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183056	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs10186080	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs10190674	1.00[CHB][hapmap]
rs10192800	1.00[CHB][hapmap]
rs10194216	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203965	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs10204415	1.00[CHB][hapmap]
rs10206555	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs10207299	1.00[CHB][hapmap]
rs10460572	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs10865391	1.00[CHB][hapmap]
rs10865392	0.84[GIH][hapmap]
rs11126366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126370	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs11126373	1.00[CHB][hapmap]
rs11126374	1.00[CHB][hapmap]
rs11126376	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11686713	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[ASN][1000 genomes]
rs11690734	1.00[CHB][hapmap]
rs11694921	1.00[CHB][hapmap]
rs11902025	1.00[CHB][hapmap]
rs12052508	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12466613	1.00[CHB][hapmap]
rs12467816	1.00[CHB][hapmap]
rs12468057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12471136	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs12471312	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];1.00[ASN][1000 genomes]
rs12471875	1.00[CHB][hapmap]
rs12476130	1.00[CHB][hapmap]
rs12476397	1.00[CHB][hapmap]
rs12618390	1.00[CHB][hapmap]
rs12713772	1.00[CHB][hapmap]
rs12713773	1.00[CHB][hapmap]
rs12992973	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12998681	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs13008041	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs13008258	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs13011477	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13383535	1.00[CHB][hapmap]
rs13390754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409513	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs13409641	1.00[CHB][hapmap]
rs13432350	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap]
rs1400581	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1400582	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs1446888	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs1446890	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs1446891	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs1446892	1.00[CHB][hapmap]
rs1446893	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs1517181	1.00[CHB][hapmap]
rs1517185	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1568145	1.00[CHB][hapmap]
rs1596930	1.00[ASN][1000 genomes]
rs1596931	1.00[ASN][1000 genomes]
rs1711838	1.00[CHB][hapmap]
rs1947118	1.00[ASN][1000 genomes]
rs2109960	1.00[CHB][hapmap]
rs2138683	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs2192014	1.00[CHB][hapmap]
rs2192015	1.00[CHB][hapmap];1.00[LWK][hapmap]
rs2203679	1.00[CHB][hapmap];0.89[GIH][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs2420444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901146	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3115351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4364045	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4852286	1.00[CHB][hapmap]
rs4852287	1.00[CHB][hapmap]
rs4852288	1.00[CHB][hapmap]
rs4852291	1.00[CHB][hapmap]
rs4852872	1.00[CHB][hapmap]
rs4852873	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs4852874	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4852875	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs4852876	1.00[CHB][hapmap]
rs4852877	1.00[CHB][hapmap]
rs4852878	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs4852883	1.00[ASN][1000 genomes]
rs57270251	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs583119	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583673	1.00[CHB][hapmap]
rs584522	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585653	1.00[CHB][hapmap]
rs585938	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs587431	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs587744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589547	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs590252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590345	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs598138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602465	1.00[CHB][hapmap]
rs613880	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs614653	1.00[CHB][hapmap]
rs620770	1.00[ASN][1000 genomes]
rs625434	1.00[CHB][hapmap]
rs628432	1.00[CEU][hapmap];1.00[CHB][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]
rs630241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632670	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs634476	1.00[CHB][hapmap]
rs634574	1.00[CHB][hapmap]
rs634586	1.00[ASN][1000 genomes]
rs634785	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs634929	1.00[CHB][hapmap]
rs636319	1.00[CHB][hapmap]
rs636734	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs638854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641123	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs641939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645489	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs646357	1.00[CHB][hapmap]
rs647242	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs647269	1.00[CHB][hapmap]
rs650352	1.00[CHB][hapmap]
rs653220	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[ASN][1000 genomes]
rs6546753	0.81[ASW][hapmap]
rs6546756	1.00[CHB][hapmap]
rs6546759	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546760	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546765	1.00[CHB][hapmap]
rs6546777	1.00[CHB][hapmap]
rs6546778	1.00[CHB][hapmap]
rs656370	1.00[CHB][hapmap]
rs656440	1.00[CHB][hapmap]
rs658067	1.00[CHB][hapmap]
rs659833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663218	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666233	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666361	1.00[CHB][hapmap]
rs668586	1.00[ASN][1000 genomes]
rs669074	1.00[CHB][hapmap]
rs6711265	1.00[ASN][1000 genomes]
rs6714312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714419	1.00[ASN][1000 genomes]
rs6714595	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs671721	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs6727607	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6729863	1.00[CHB][hapmap]
rs6733210	1.00[CHB][hapmap]
rs6737565	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742264	1.00[CHB][hapmap]
rs6742312	1.00[CHB][hapmap]
rs6747378	1.00[CHB][hapmap]
rs674863	1.00[CHB][hapmap]
rs6750766	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs6752122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753073	1.00[CHB][hapmap]
rs6758462	1.00[CHB][hapmap]
rs6758593	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[ASN][1000 genomes]
rs678684	1.00[CHB][hapmap]
rs680380	1.00[CHB][hapmap]
rs680495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681574	1.00[CHB][hapmap]
rs683328	1.00[CHB][hapmap]
rs684673	1.00[CHB][hapmap]
rs687325	1.00[CHB][hapmap]
rs687371	1.00[CHB][hapmap]
rs688433	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs689154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420588	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420667	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7558686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559131	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[MKK][hapmap]
rs7560529	1.00[CHB][hapmap]
rs7563738	1.00[ASN][1000 genomes]
rs7565198	1.00[CHB][hapmap]
rs7568803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577238	1.00[CHB][hapmap]
rs7577877	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7580952	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583271	1.00[CHB][hapmap]
rs7591025	1.00[CHB][hapmap]
rs7591303	1.00[CHB][hapmap]
rs7594350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595180	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595315	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598238	1.00[CHB][hapmap]
rs7600273	1.00[ASN][1000 genomes]
rs7601020	1.00[CHB][hapmap];0.84[GIH][hapmap]
rs7601318	1.00[CHB][hapmap]
rs7603966	1.00[CHB][hapmap]
rs9309464	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983928	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963919	chr2:72372956-72830387	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1005487	chr2:72464784-72819704	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv999179	chr2:72561463-72761103	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1008335	chr2:72561463-72819704	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3429281	chr2:72590346-72623676	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv874264	chr2:72593243-72901170	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv2773	chr2:72603908-72649311	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs642652	CST8	trans	cerebellum	SCAN
rs642652	MPHOSPH10	cis	cerebellum	SCAN
rs642652	TGFA	cis	cerebellum	SCAN
rs642652	AUP1	cis	parietal	SCAN
rs642652	INO80B	cis	parietal	SCAN
rs642652	FBXO48	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72613800-72654000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr2:72619600-72625400	Weak transcription	Aorta	Aorta
3	chr2:72619600-72640600	Weak transcription	Ovary	ovary
4	chr2:72621400-72622800	Enhancers	Fetal Lung	lung
5	chr2:72621400-72622800	Enhancers	A549	lung

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