Variant report

Variant	rs2966
Chromosome Location	chr6:33689520-33689521
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	chr6:33687230..33690069-chr6:34119183..34120791,2	MCF-7	breast:
2	chr6:33678022..33679887-chr6:33687741..33690570,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1014933	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10947430	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10947434	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10947435	1.00[ASW][hapmap];0.90[CHB][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11759396	0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1555965	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2147656	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2147657	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2229642	0.92[EUR][1000 genomes]
rs2274458	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281829	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2296736	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296738	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2296739	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2296741	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2296742	0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs28651968	0.83[AMR][1000 genomes]
rs3227	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818521	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3818523	0.93[EUR][1000 genomes]
rs3818524	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3818525	0.93[EUR][1000 genomes]
rs3818527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818529	0.93[EUR][1000 genomes]
rs3818530	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4711336	1.00[ASW][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4711337	0.92[EUR][1000 genomes]
rs4711338	0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4711339	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4711340	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4711343	0.90[ASW][hapmap];0.90[CHB][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713655	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4713658	0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs4713659	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713660	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713663	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4713665	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4713666	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4713667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713669	0.89[EUR][1000 genomes]
rs4713670	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713671	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4713672	0.80[CHB][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4713674	0.90[ASW][hapmap];0.80[CHB][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4713675	0.90[CHB][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs509539	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs542441	0.85[CHD][hapmap]
rs560111	0.90[CHB][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60704560	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs622917	0.88[GIH][hapmap]
rs6457739	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.83[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6904816	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6916949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928010	0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6938056	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs749338	0.88[ASW][hapmap];0.84[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs749847	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753890	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs754404	0.93[EUR][1000 genomes]
rs764752	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs764754	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7739505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7759668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770465	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791902	0.82[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs791903	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9348924	0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9348925	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9366828	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9368773	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9368776	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9380375	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394162	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9394163	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942640	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942643	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9469566	0.81[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
2	nsv830639	chr6:33592022-33711346	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
3	nsv885772	chr6:33638180-33767727	Bivalent Enhancer Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Educational attainment	25201988	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2966	ITPR3	cis	Whole Blood	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33680000-33690000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:33680000-33690200	Weak transcription	Psoas Muscle	Psoas
3	chr6:33680000-33693000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:33680000-33695200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:33680000-33695800	Weak transcription	Spleen	Spleen
6	chr6:33680000-33696200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:33680000-33698400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:33680000-33705000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:33685200-33693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:33686200-33700200	Weak transcription	Liver	Liver
11	chr6:33686400-33689600	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:33686400-33689600	Weak transcription	Placenta	Placenta
13	chr6:33686400-33691600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:33686400-33691800	Weak transcription	Colon Smooth Muscle	Colon
15	chr6:33686400-33710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:33686600-33689600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:33686600-33689600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:33686600-33689800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:33686600-33690000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:33686600-33690600	Weak transcription	Right Ventricle	heart
21	chr6:33686600-33695800	Weak transcription	Right Atrium	heart
22	chr6:33686600-33698600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:33687400-33691200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:33687400-33692600	Enhancers	Stomach Mucosa	stomach
25	chr6:33687400-33694000	Weak transcription	Brain Anterior Caudate	brain
26	chr6:33687800-33693200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:33688000-33692000	Weak transcription	Brain Substantia Nigra	brain
28	chr6:33688200-33689600	Weak transcription	Fetal Brain Male	brain
29	chr6:33688200-33690200	Weak transcription	Fetal Lung	lung
30	chr6:33688600-33690000	Enhancers	Primary B cells from peripheral blood	blood
31	chr6:33688800-33689800	Strong transcription	Left Ventricle	heart
32	chr6:33688800-33690000	Weak transcription	Gastric	stomach
33	chr6:33688800-33698200	Weak transcription	Lung	lung
34	chr6:33688800-33700000	Strong transcription	HSMM	muscle
35	chr6:33689200-33689600	Weak transcription	Pancreas	Pancrea
36	chr6:33689200-33696800	Strong transcription	HSMMtube	muscle
37	chr6:33689400-33689600	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
38	chr6:33689400-33689800	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr6:33689400-33695000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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