Variant report

Variant	rs263977
Chromosome Location	chr1:45360287-45360288
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:45357545..45362939-chr1:45366280..45371590,5	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10158188	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10465818	0.81[ASW][hapmap];0.91[GIH][hapmap];0.80[MKK][hapmap]
rs11211031	0.81[ASW][hapmap]
rs11211037	0.96[CEU][hapmap];0.94[GIH][hapmap];0.92[TSI][hapmap]
rs11211044	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11211046	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11211047	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11573543	0.87[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11577974	0.84[CEU][hapmap]
rs11584031	0.96[CEU][hapmap]
rs12059964	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap]
rs12094007	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12118515	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12120470	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144803	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1226572	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs12408818	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12568071	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12568279	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2273940	0.89[EUR][1000 genomes]
rs263956	0.85[ASN][1000 genomes]
rs263962	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263965	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs263966	0.86[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs263975	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][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]
rs263980	0.86[ASN][1000 genomes]
rs263982	0.82[ASN][1000 genomes]
rs263987	0.87[ASN][1000 genomes]
rs263990	0.86[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs263998	0.81[ASN][1000 genomes]
rs264005	0.85[ASN][1000 genomes]
rs264009	0.86[ASN][1000 genomes]
rs264011	0.86[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs264014	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2983715	0.82[JPT][hapmap]
rs3121173	0.86[ASN][1000 genomes]
rs36107413	0.86[ASN][1000 genomes]
rs3795720	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs398200	0.81[ASN][1000 genomes]
rs399628	0.81[ASN][1000 genomes]
rs401665	0.81[ASN][1000 genomes]
rs438493	0.86[ASN][1000 genomes]
rs452989	0.86[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs620764	0.82[ASN][1000 genomes]
rs6429548	0.82[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs6688465	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696675	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6698951	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs746320	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7514741	0.87[EUR][1000 genomes]
rs7525308	0.81[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]
rs7526786	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7545808	0.89[EUR][1000 genomes]
rs7554177	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs932691	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9429058	0.86[ASN][1000 genomes]
rs9645347	0.89[EUR][1000 genomes]
rs9988451	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
2	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
3	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
4	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs263977	CTPS	cis	cerebellum	SCAN
rs263977	C1orf84	cis	parietal	SCAN
rs263977	EIF2B3	cis	parietal	SCAN
rs263977	EIF2B3	cis	cerebellum	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45309200-45360600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:45334600-45371800	Weak transcription	Gastric	stomach
3	chr1:45340800-45361800	Weak transcription	Aorta	Aorta
4	chr1:45345600-45366200	Weak transcription	Esophagus	oesophagus
5	chr1:45345800-45363600	Weak transcription	Colonic Mucosa	Colon
6	chr1:45346400-45363200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:45347600-45360400	Weak transcription	HMEC	breast
8	chr1:45347600-45362600	Weak transcription	Lung	lung
9	chr1:45347600-45410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:45350600-45360600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:45350600-45361200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:45350800-45363200	Weak transcription	Right Ventricle	heart
13	chr1:45350800-45363400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:45350800-45364200	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:45350800-45369000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:45350800-45382400	Weak transcription	Pancreas	Pancrea
17	chr1:45350800-45411800	Weak transcription	Left Ventricle	heart
18	chr1:45352600-45360400	Weak transcription	Ovary	ovary
19	chr1:45353000-45374000	Weak transcription	Fetal Heart	heart
20	chr1:45355200-45366400	Weak transcription	Psoas Muscle	Psoas
21	chr1:45355600-45368200	Weak transcription	Fetal Stomach	stomach
22	chr1:45355800-45363800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:45355800-45369000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:45355800-45411200	Weak transcription	Fetal Lung	lung
25	chr1:45356000-45363600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:45356000-45369000	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:45356000-45373000	Weak transcription	Brain Anterior Caudate	brain
28	chr1:45356000-45407000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:45356000-45423800	Weak transcription	Thymus	Thymus
30	chr1:45356400-45390600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:45356600-45362600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:45356600-45364000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:45356800-45374600	Weak transcription	Spleen	Spleen
34	chr1:45357200-45361000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:45357200-45361800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:45357200-45365000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:45357200-45388400	Weak transcription	Fetal Intestine Large	intestine
38	chr1:45357400-45360800	Strong transcription	Primary B cells from cord blood	blood
39	chr1:45357400-45364400	Weak transcription	Fetal Brain Male	brain
40	chr1:45357400-45365400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:45357400-45390600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:45357400-45411800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:45357600-45365600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:45357600-45391600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:45357800-45360400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:45357800-45368200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:45357800-45391000	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr1:45358000-45360400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:45358000-45360400	Strong transcription	K562	blood
50	chr1:45358000-45361800	Weak transcription	Primary B cells from peripheral blood	blood

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