Variant report

Variant	rs7559131
Chromosome Location	chr2:72518970-72518971
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:72518926..72520501-chr2:72530271..72532810,2	K562	blood:

Extended variants
information (count: 159 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs1003672	0.87[EUR][1000 genomes]
rs10168145	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173381	0.80[ASW][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap]
rs10175915	0.91[GIH][hapmap]
rs10183056	1.00[CHB][hapmap]
rs10186080	1.00[CHB][hapmap]
rs10190674	1.00[CHB][hapmap]
rs10192800	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10196589	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs10203965	1.00[CHB][hapmap]
rs10204415	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap]
rs10205108	0.85[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs10206555	1.00[CHB][hapmap]
rs10207299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221769	0.85[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs11126363	0.83[EUR][1000 genomes]
rs11126366	1.00[CHB][hapmap]
rs1159763	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1159764	0.85[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs1159765	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1159766	0.85[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs11690734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12466613	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12467816	1.00[CHB][hapmap]
rs12468057	1.00[CHB][hapmap]
rs12471875	1.00[CHB][hapmap]
rs12476397	1.00[CHB][hapmap]
rs13383535	1.00[CHB][hapmap]
rs13390754	1.00[CHB][hapmap]
rs13409513	1.00[CHB][hapmap]
rs13409641	1.00[CHB][hapmap]
rs13417114	0.83[GIH][hapmap]
rs13418637	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs13432350	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400582	1.00[CHB][hapmap]
rs1568145	1.00[CHB][hapmap]
rs1711838	1.00[CHB][hapmap]
rs17673916	0.87[GIH][hapmap]
rs17724860	0.91[GIH][hapmap]
rs17725024	0.91[GIH][hapmap]
rs194235	0.87[GIH][hapmap]
rs2041563	0.87[GIH][hapmap]
rs2109960	1.00[CHB][hapmap]
rs2109961	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109963	0.87[GIH][hapmap]
rs2192014	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2192015	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[ASN][1000 genomes]
rs2203679	1.00[CHB][hapmap]
rs2420442	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420444	1.00[CHB][hapmap]
rs2901144	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901146	1.00[CHB][hapmap]
rs3115351	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[MKK][hapmap]
rs41386	0.91[GIH][hapmap]
rs41388	0.95[GIH][hapmap];0.81[TSI][hapmap]
rs41389	0.95[GIH][hapmap];0.81[TSI][hapmap]
rs41393	0.95[GIH][hapmap]
rs41394	0.95[GIH][hapmap];0.81[TSI][hapmap]
rs41398	0.91[GIH][hapmap]
rs41401	0.87[GIH][hapmap]
rs41402	0.87[GIH][hapmap]
rs41403	0.95[GIH][hapmap]
rs41407	0.95[GIH][hapmap]
rs41412	0.91[GIH][hapmap];0.81[TSI][hapmap]
rs41415	0.87[GIH][hapmap]
rs41416	0.87[GIH][hapmap]
rs41417	0.91[GIH][hapmap]
rs4852286	1.00[CHB][hapmap];0.91[GIH][hapmap]
rs4852287	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs4852288	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583673	1.00[CHB][hapmap]
rs585653	1.00[CHB][hapmap]
rs585938	1.00[CHB][hapmap]
rs587431	1.00[CHB][hapmap]
rs587744	1.00[CHB][hapmap]
rs589547	1.00[CHB][hapmap]
rs590252	1.00[CHB][hapmap]
rs590345	1.00[CHB][hapmap]
rs598138	1.00[CHB][hapmap]
rs598496	1.00[CHB][hapmap]
rs602465	1.00[CHB][hapmap]
rs613880	1.00[CHB][hapmap]
rs614653	1.00[CHB][hapmap]
rs625434	1.00[CHB][hapmap]
rs628432	1.00[CHB][hapmap]
rs630241	1.00[CHB][hapmap]
rs632670	1.00[CHB][hapmap]
rs634476	1.00[CHB][hapmap]
rs634574	1.00[CHB][hapmap]
rs634785	1.00[CHB][hapmap]
rs634929	1.00[CHB][hapmap]
rs636319	1.00[CHB][hapmap]
rs636734	1.00[CHB][hapmap]
rs638854	1.00[CHB][hapmap]
rs640610	1.00[CHB][hapmap]
rs641123	1.00[CHB][hapmap]
rs641939	0.91[ASW][hapmap];1.00[CHB][hapmap]
rs642652	0.91[ASW][hapmap];1.00[CHB][hapmap];0.89[MKK][hapmap]
rs645489	1.00[CHB][hapmap]
rs646357	1.00[CHB][hapmap]
rs647242	1.00[CHB][hapmap]
rs647269	1.00[CHB][hapmap]
rs650352	1.00[CHB][hapmap]
rs653220	1.00[CHB][hapmap]
rs6546752	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs6546753	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs6546756	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546760	1.00[CHB][hapmap]
rs6546764	1.00[CHB][hapmap]
rs6546765	1.00[CHB][hapmap]
rs656370	1.00[CHB][hapmap]
rs656440	1.00[CHB][hapmap]
rs658067	1.00[CHB][hapmap]
rs659833	1.00[CHB][hapmap]
rs663218	0.80[ASW][hapmap];1.00[CHB][hapmap];0.87[MKK][hapmap]
rs666233	0.91[ASW][hapmap];1.00[CHB][hapmap];0.96[MKK][hapmap]
rs666361	1.00[CHB][hapmap]
rs669074	1.00[CHB][hapmap]
rs6709109	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709114	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6711265	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6714595	1.00[CHB][hapmap]
rs671721	1.00[CHB][hapmap]
rs6722637	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733210	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6742264	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674863	1.00[CHB][hapmap]
rs6752122	1.00[CHB][hapmap]
rs6753073	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758593	1.00[CHB][hapmap]
rs6760895	0.87[GIH][hapmap]
rs678684	1.00[CHB][hapmap]
rs680380	1.00[CHB][hapmap]
rs680495	1.00[CHB][hapmap]
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[CHB][hapmap]
rs719118	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558686	1.00[CHB][hapmap]
rs7558919	1.00[CHB][hapmap]
rs7565922	0.87[GIH][hapmap]
rs7568803	1.00[CHB][hapmap]
rs7577877	1.00[CHB][hapmap]
rs7583271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594350	1.00[CHB][hapmap]
rs7595180	1.00[CHB][hapmap]
rs7603966	1.00[CHB][hapmap]
rs9309463	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs9309464	0.80[ASW][hapmap];1.00[CHB][hapmap];0.85[MKK][hapmap];0.81[TSI][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7559131	CCT7	cis	parietal	SCAN
rs7559131	C20orf24	trans	cerebellum	SCAN
rs7559131	MPHOSPH10	cis	cerebellum	SCAN
rs7559131	PCYOX1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72517000-72520600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:72517400-72521000	Weak transcription	NHDF-Ad	bronchial
3	chr2:72517800-72520600	Enhancers	A549	lung
4	chr2:72518200-72519000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:72518600-72519200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:72518600-72520600	Weak transcription	Osteobl	bone
7	chr2:72518800-72520800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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