Variant report

Variant	rs4852288
Chromosome Location	chr2:72505475-72505476
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 149 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs1003672	0.90[EUR][1000 genomes]
rs10168145	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173381	1.00[CHB][hapmap]
rs10175915	0.91[GIH][hapmap]
rs10186080	1.00[CHB][hapmap]
rs10190674	1.00[CHB][hapmap]
rs10192800	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10196589	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs10203965	1.00[CHB][hapmap]
rs10204415	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap]
rs10205108	0.90[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs10207299	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10221769	0.90[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs11126363	0.86[EUR][1000 genomes]
rs11126366	1.00[CHB][hapmap]
rs1159763	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs1159764	0.90[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1159765	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs1159766	0.90[CEU][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs11690734	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694921	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902025	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12466613	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][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	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs13432350	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400582	1.00[CHB][hapmap]
rs1568145	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	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.96[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	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420444	1.00[CHB][hapmap]
rs2901144	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2901146	1.00[CHB][hapmap]
rs3115351	1.00[CHB][hapmap]
rs41386	0.91[GIH][hapmap]
rs41388	0.95[GIH][hapmap]
rs41389	0.95[GIH][hapmap]
rs41393	0.95[GIH][hapmap]
rs41394	0.95[GIH][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]
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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs585653	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	1.00[CHB][hapmap]
rs642652	1.00[CHB][hapmap]
rs645489	1.00[CHB][hapmap]
rs646357	1.00[CHB][hapmap]
rs647242	1.00[CHB][hapmap]
rs647269	1.00[CHB][hapmap]
rs6546752	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs6546753	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs6546756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[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	1.00[CHB][hapmap]
rs666233	1.00[CHB][hapmap]
rs666361	1.00[CHB][hapmap]
rs669074	1.00[CHB][hapmap]
rs6709109	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709114	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6711265	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs671721	1.00[CHB][hapmap]
rs6722637	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729863	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733210	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs6742264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674863	1.00[CHB][hapmap]
rs6752122	1.00[CHB][hapmap]
rs6753073	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758462	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
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]
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	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558686	1.00[CHB][hapmap]
rs7558919	1.00[CHB][hapmap]
rs7559131	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]
rs7565922	0.87[GIH][hapmap]
rs7568803	1.00[CHB][hapmap]
rs7577877	1.00[CHB][hapmap]
rs7583271	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594350	1.00[CHB][hapmap]
rs7595180	1.00[CHB][hapmap]
rs7603966	1.00[CHB][hapmap]
rs9309463	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs9309464	1.00[CHB][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
rs4852288	MPHOSPH10	cis	cerebellum	SCAN
rs4852288	C20orf24	trans	cerebellum	SCAN
rs4852288	CCT7	cis	parietal	SCAN
rs4852288	PCYOX1	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72489200-72508200	Weak transcription	Aorta	Aorta
2	chr2:72499400-72507800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:72499400-72507800	Weak transcription	Psoas Muscle	Psoas
4	chr2:72499600-72510400	Weak transcription	Right Ventricle	heart
5	chr2:72501000-72505800	Weak transcription	Pancreas	Pancrea
6	chr2:72502800-72505800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:72502800-72507800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:72502800-72507800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:72503000-72505600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:72503000-72506200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:72503200-72505600	Enhancers	Osteobl	bone
12	chr2:72503800-72505600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:72503800-72505600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:72504000-72505600	Enhancers	NHDF-Ad	bronchial
15	chr2:72504200-72508000	Weak transcription	Ovary	ovary
16	chr2:72504800-72513200	Weak transcription	Left Ventricle	heart
17	chr2:72505000-72505800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:72505200-72505600	Enhancers	Hela-S3	cervix
19	chr2:72505200-72505600	Enhancers	NHEK	skin
20	chr2:72505200-72505800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:72505200-72505800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:72505200-72505800	Enhancers	A549	lung
23	chr2:72505200-72506400	Enhancers	Fetal Heart	heart
24	chr2:72505400-72505600	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:72505400-72505600	Enhancers	Small Intestine	intestine
26	chr2:72505400-72505600	Enhancers	NH-A	brain
27	chr2:72505400-72505800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr2:72505400-72505800	Enhancers	NHLF	lung
29	chr2:72505400-72506400	Enhancers	Skeletal Muscle Male	skeletal muscle

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