Variant report

Variant	rs263975
Chromosome Location	chr1:45358527-45358528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45357545..45362939-chr1:45366280..45371590,5	K562	blood:
2	chr1:45285269..45287517-chr1:45356537..45358662,2	K562	blood:
3	chr1:45348967..45351344-chr1:45356459..45358965,2	K562	blood:
4	chr1:45185573..45188435-chr1:45355678..45358866,3	K562	blood:

Variant related genes	Relation type
ENSG00000202444	Chromatin interaction
ENSG00000199377	Chromatin interaction

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]
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];0.98[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];0.83[MKK][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs263977	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];0.80[MEX][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	0.81[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];0.86[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];0.80[MEX][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];0.98[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
rs263975	EIF2B3	cis	cerebellum	SCAN
rs263975	CTPS	cis	cerebellum	SCAN
rs263975	C1orf84	cis	parietal	SCAN
rs263975	EIF2B3	cis	parietal	SCAN

Chromatin state (count:99 , 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	chr1:45313400-45360200	Weak transcription	Hela-S3	cervix
3	chr1:45322600-45360000	Weak transcription	Small Intestine	intestine
4	chr1:45334600-45371800	Weak transcription	Gastric	stomach
5	chr1:45340800-45361800	Weak transcription	Aorta	Aorta
6	chr1:45345600-45366200	Weak transcription	Esophagus	oesophagus
7	chr1:45345800-45363600	Weak transcription	Colonic Mucosa	Colon
8	chr1:45346200-45359200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:45346400-45363200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:45347600-45358800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:45347600-45360400	Weak transcription	HMEC	breast
12	chr1:45347600-45362600	Weak transcription	Lung	lung
13	chr1:45347600-45410800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:45348000-45360000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:45349600-45360000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:45350600-45360600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:45350600-45361200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:45350800-45363200	Weak transcription	Right Ventricle	heart
19	chr1:45350800-45363400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:45350800-45364200	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:45350800-45369000	Weak transcription	Brain Angular Gyrus	brain
22	chr1:45350800-45382400	Weak transcription	Pancreas	Pancrea
23	chr1:45350800-45411800	Weak transcription	Left Ventricle	heart
24	chr1:45351800-45358600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:45352600-45360400	Weak transcription	Ovary	ovary
26	chr1:45353000-45374000	Weak transcription	Fetal Heart	heart
27	chr1:45354800-45359600	Weak transcription	Osteobl	bone
28	chr1:45354800-45360000	Weak transcription	NHEK	skin
29	chr1:45355200-45366400	Weak transcription	Psoas Muscle	Psoas
30	chr1:45355600-45368200	Weak transcription	Fetal Stomach	stomach
31	chr1:45355800-45360000	Weak transcription	HUVEC	blood vessel
32	chr1:45355800-45363800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:45355800-45369000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:45355800-45411200	Weak transcription	Fetal Lung	lung
35	chr1:45356000-45359200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:45356000-45360000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:45356000-45363600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr1:45356000-45369000	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:45356000-45373000	Weak transcription	Brain Anterior Caudate	brain
40	chr1:45356000-45407000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:45356000-45423800	Weak transcription	Thymus	Thymus
42	chr1:45356400-45390600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:45356600-45358800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:45356600-45359600	Weak transcription	NHLF	lung
45	chr1:45356600-45360200	Weak transcription	NHDF-Ad	bronchial
46	chr1:45356600-45362600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:45356600-45364000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:45356800-45358800	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:45356800-45359400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:45356800-45374600	Weak transcription	Spleen	Spleen

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