Variant report

Variant	rs7558686
Chromosome Location	chr2:72578789-72578790
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 166 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:162)

rs_ID	r²[population]
rs10168145	1.00[CHB][hapmap]
rs10173381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10183056	1.00[CHB][hapmap]
rs10186080	1.00[CHB][hapmap];0.90[GIH][hapmap]
rs10190674	1.00[CHB][hapmap]
rs10192800	1.00[CHB][hapmap]
rs10194216	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203965	1.00[CHB][hapmap];0.89[GIH][hapmap]
rs10204415	1.00[CHB][hapmap]
rs10206555	1.00[CHB][hapmap]
rs10207299	1.00[CHB][hapmap]
rs10460572	1.00[CHB][hapmap]
rs10865391	1.00[CHB][hapmap]
rs11126366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126370	1.00[CHB][hapmap]
rs11126373	1.00[CHB][hapmap]
rs11126376	1.00[ASN][1000 genomes]
rs11686713	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];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12471312	1.00[ASN][1000 genomes]
rs12471875	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]
rs13011477	1.00[ASN][1000 genomes]
rs13383535	1.00[CHB][hapmap]
rs13390754	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409513	1.00[CHB][hapmap];0.90[GIH][hapmap]
rs13409641	1.00[CHB][hapmap]
rs13432350	1.00[CHB][hapmap]
rs1400581	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1400582	1.00[CHB][hapmap];0.85[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]
rs2192014	1.00[CHB][hapmap]
rs2192015	1.00[CHB][hapmap]
rs2203679	1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[ASN][1000 genomes]
rs2420444	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901146	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3115351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4364045	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];0.90[GIH][hapmap];1.00[ASN][1000 genomes]
rs4852874	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4852875	1.00[CHB][hapmap]
rs4852876	1.00[CHB][hapmap]
rs4852877	1.00[CHB][hapmap]
rs57270251	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs583119	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583673	1.00[CHB][hapmap]
rs584522	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585653	1.00[CHB][hapmap]
rs585938	1.00[CHB][hapmap]
rs587431	1.00[CHB][hapmap];0.90[GIH][hapmap]
rs587744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589547	1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs590252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602465	1.00[CHB][hapmap]
rs613880	1.00[CHB][hapmap];0.90[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];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632670	1.00[CHB][hapmap]
rs634476	1.00[CHB][hapmap]
rs634574	1.00[CHB][hapmap]
rs634586	1.00[ASN][1000 genomes]
rs634785	1.00[CHB][hapmap];0.90[GIH][hapmap]
rs634929	1.00[CHB][hapmap]
rs636319	1.00[CHB][hapmap]
rs636734	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs638854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641123	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs641939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642652	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]
rs645489	1.00[CHB][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];0.90[GIH][hapmap];1.00[ASN][1000 genomes]
rs6546756	1.00[CHB][hapmap]
rs6546759	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546760	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546765	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];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663218	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs666361	1.00[CHB][hapmap]
rs668586	1.00[ASN][1000 genomes]
rs669074	1.00[CHB][hapmap]
rs6711265	1.00[ASN][1000 genomes]
rs6714312	0.91[AMR][1000 genomes];0.96[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]
rs6727607	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6729863	1.00[CHB][hapmap]
rs6733210	1.00[CHB][hapmap]
rs6737565	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742264	1.00[CHB][hapmap]
rs6742312	1.00[CHB][hapmap]
rs674863	1.00[CHB][hapmap]
rs6750766	1.00[CHB][hapmap]
rs6752122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6753073	1.00[CHB][hapmap]
rs6758462	1.00[CHB][hapmap]
rs6758593	1.00[CHB][hapmap];0.90[GIH][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];0.93[AMR][1000 genomes];0.98[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]
rs689154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420588	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420667	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7558919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559131	1.00[CHB][hapmap]
rs7563738	1.00[ASN][1000 genomes]
rs7568803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577877	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7580952	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583271	1.00[CHB][hapmap]
rs7594350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595180	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595315	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603966	1.00[CHB][hapmap]
rs9309464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983928	1.00[CHB][hapmap]

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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7558686	INO80B	cis	parietal	SCAN
rs7558686	FBXO48	cis	cerebellum	SCAN
rs7558686	AUP1	cis	parietal	SCAN
rs7558686	STAMBP	cis	cerebellum	SCAN
rs7558686	MPHOSPH10	cis	cerebellum	SCAN
rs7558686	TGFA	cis	cerebellum	SCAN
rs7558686	CST8	trans	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72531200-72594800	Weak transcription	Esophagus	oesophagus
2	chr2:72553800-72594600	Weak transcription	Aorta	Aorta
3	chr2:72559200-72607400	Weak transcription	Liver	Liver
4	chr2:72560600-72594800	Weak transcription	Pancreas	Pancrea
5	chr2:72572200-72601400	Weak transcription	Adipose Nuclei	Adipose
6	chr2:72572200-72607200	Weak transcription	Psoas Muscle	Psoas
7	chr2:72573600-72595000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:72574200-72594800	Weak transcription	Placenta	Placenta
9	chr2:72575200-72588800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:72576600-72581600	Weak transcription	Fetal Heart	heart
11	chr2:72576600-72594800	Weak transcription	Right Ventricle	heart
12	chr2:72576600-72605200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:72577200-72578800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:72577400-72579400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr2:72577600-72579000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr2:72577600-72579200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:72577600-72579400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:72577800-72578800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:72577800-72578800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:72577800-72578800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:72577800-72578800	Enhancers	HMEC	breast
22	chr2:72577800-72579000	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr2:72577800-72579000	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr2:72578000-72578800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:72578000-72579000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr2:72578000-72606400	Weak transcription	HSMM	muscle
27	chr2:72578200-72579200	Enhancers	NHEK	skin

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