Variant report

Variant	rs666233
Chromosome Location	chr2:72602388-72602389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 181 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:175)

rs_ID	r²[population]
rs10168145	1.00[CHB][hapmap]
rs10173381	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.94[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	0.81[AMR][1000 genomes];0.91[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];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126370	1.00[CHB][hapmap]
rs11126373	1.00[CHB][hapmap]
rs11126374	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];0.93[EUR][1000 genomes]
rs12471136	1.00[CHB][hapmap]
rs12471312	1.00[CHB][hapmap];0.90[GIH][hapmap];0.80[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]
rs13008041	1.00[CHB][hapmap]
rs13008258	1.00[CHB][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];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409513	1.00[CHB][hapmap];0.90[GIH][hapmap]
rs13409641	1.00[CHB][hapmap]
rs13432350	0.91[ASW][hapmap];1.00[CHB][hapmap]
rs1400581	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1400582	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs1446888	1.00[CHB][hapmap]
rs1446890	1.00[CHB][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];0.88[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];0.95[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[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];0.90[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]
rs4852878	1.00[CHB][hapmap]
rs57270251	0.94[EUR][1000 genomes]
rs583119	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583673	1.00[CHB][hapmap]
rs584522	0.84[AMR][1000 genomes];0.90[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];1.00[YRI][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];0.96[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];0.89[AMR][1000 genomes];0.96[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];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[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];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641123	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs641939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642652	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]
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]
rs6546753	0.81[ASW][hapmap]
rs6546756	1.00[CHB][hapmap]
rs6546759	0.81[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]
rs656370	1.00[CHB][hapmap]
rs656440	1.00[CHB][hapmap]
rs658067	1.00[CHB][hapmap]
rs659833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[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];0.95[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[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	0.93[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]
rs6727607	0.85[EUR][1000 genomes]
rs6729863	1.00[CHB][hapmap]
rs6733210	1.00[CHB][hapmap]
rs6737565	0.81[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]
rs6752122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[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];0.90[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];0.91[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]
rs689154	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420588	0.81[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];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]
rs7558919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7559131	0.91[ASW][hapmap];1.00[CHB][hapmap];0.96[MKK][hapmap]
rs7560529	1.00[CHB][hapmap]
rs7563738	1.00[ASN][1000 genomes]
rs7568803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[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	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583271	1.00[CHB][hapmap]
rs7594350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595180	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595315	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601020	1.00[CHB][hapmap]
rs7603966	1.00[CHB][hapmap]
rs9309464	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983928	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs666233	AUP1	cis	parietal	SCAN
rs666233	CST8	trans	cerebellum	SCAN
rs666233	FBXO48	cis	cerebellum	SCAN
rs666233	TGFA	cis	cerebellum	SCAN
rs666233	INO80B	cis	parietal	SCAN
rs666233	MPHOSPH10	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72559200-72607400	Weak transcription	Liver	Liver
2	chr2:72572200-72607200	Weak transcription	Psoas Muscle	Psoas
3	chr2:72576600-72605200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr2:72578000-72606400	Weak transcription	HSMM	muscle
5	chr2:72580200-72605200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:72581600-72607800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:72582600-72605400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:72590200-72604200	Weak transcription	Brain Hippocampus Middle	brain
9	chr2:72592600-72613400	Weak transcription	Gastric	stomach
10	chr2:72594200-72608400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:72594400-72607200	Weak transcription	Brain Substantia Nigra	brain
12	chr2:72595000-72605200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:72595000-72613400	Weak transcription	Aorta	Aorta
14	chr2:72595000-72613600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:72595200-72604200	Weak transcription	Placenta	Placenta
16	chr2:72595200-72605400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr2:72595200-72606800	Weak transcription	Lung	lung
18	chr2:72595200-72608600	Weak transcription	NHEK	skin
19	chr2:72595200-72613400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:72595200-72613400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:72595200-72613400	Weak transcription	Fetal Stomach	stomach
22	chr2:72595200-72613400	Weak transcription	Pancreas	Pancrea
23	chr2:72595200-72613400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr2:72595200-72613600	Weak transcription	Right Ventricle	heart
25	chr2:72595400-72613200	Weak transcription	Left Ventricle	heart
26	chr2:72595400-72613400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:72597200-72607000	Weak transcription	Fetal Brain Male	brain
28	chr2:72597400-72605200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:72597800-72606800	Weak transcription	Esophagus	oesophagus
30	chr2:72598000-72605200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:72598200-72604200	Weak transcription	Fetal Intestine Small	intestine
32	chr2:72598800-72604400	Weak transcription	Fetal Lung	lung
33	chr2:72598800-72605400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:72599200-72605400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr2:72599400-72604000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:72599600-72603600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:72599600-72605400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:72599600-72613400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:72599800-72604200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:72599800-72605600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr2:72600000-72613400	Weak transcription	Ovary	ovary
42	chr2:72600200-72604600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:72600200-72605000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:72601200-72605200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:72601200-72613400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr2:72601400-72604000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:72601400-72605400	Weak transcription	Brain Anterior Caudate	brain
48	chr2:72601600-72605200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr2:72601800-72604600	Weak transcription	Adipose Nuclei	Adipose
50	chr2:72601800-72605200	Weak transcription	Fetal Intestine Large	intestine

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