Variant report

Variant	rs1539468
Chromosome Location	chr10:93867230-93867231
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:93866014..93868686-chr10:93868973..93871759,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1059515	0.85[GIH][hapmap]
rs10786028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10882005	0.85[GIH][hapmap]
rs10882016	0.85[GIH][hapmap]
rs10882023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10882025	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882031	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs10882037	0.81[ASW][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs11186774	0.82[GIH][hapmap]
rs11186792	0.85[GIH][hapmap]
rs11186815	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11186817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11186818	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11186822	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186829	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11186830	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11186834	0.83[ASN][1000 genomes]
rs11186835	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11186836	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11186838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11186839	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11186841	0.81[ASW][hapmap];0.82[CEU][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11186843	0.82[EUR][1000 genomes]
rs11186856	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs11186879	0.87[TSI][hapmap]
rs11186884	0.87[TSI][hapmap]
rs11186894	0.87[TSI][hapmap]
rs11186898	0.87[TSI][hapmap]
rs11527871	0.81[CHB][hapmap]
rs12357187	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12571139	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];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17107517	0.81[ASW][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap]
rs1878424	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1914345	0.85[GIH][hapmap]
rs1935865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2096227	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2105364	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2185834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2421831	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2421874	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34658839	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781230	0.81[ASW][hapmap];0.82[CEU][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs3781231	0.82[EUR][1000 genomes]
rs3781233	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4933712	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4933717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56345827	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56705680	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61875208	0.80[EUR][1000 genomes]
rs6583802	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs66636110	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7067935	0.81[ASW][hapmap];0.82[CEU][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs7069149	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071524	0.82[EUR][1000 genomes]
rs7079499	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7084059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7085684	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7086446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7088903	0.87[TSI][hapmap]
rs7096357	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs766398	0.94[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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766399	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8181288	0.85[GIH][hapmap]
rs9787608	0.81[ASW][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.87[TSI][hapmap]
rs9794362	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051226	chr10:93711296-93915586	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv540745	chr10:93711296-93915586	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv895893	chr10:93747260-93875264	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv975763	chr10:93822289-94105956	Enhancers Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1539468	CPEB3	cis	parietal	SCAN
rs1539468	BTAF1	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93841200-93872400	Weak transcription	Spleen	Spleen
2	chr10:93841200-93881600	Weak transcription	Esophagus	oesophagus
3	chr10:93859200-93901400	Weak transcription	Primary B cells from cord blood	blood
4	chr10:93859400-93874800	Weak transcription	Fetal Intestine Large	intestine
5	chr10:93861000-93873600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr10:93861400-93872600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr10:93861400-93879000	Weak transcription	Adipose Nuclei	Adipose
8	chr10:93861800-93869800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:93862000-93869400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr10:93862000-93874200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr10:93862000-93881400	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:93862000-93881400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:93862000-93883200	Weak transcription	Fetal Stomach	stomach
14	chr10:93862200-93867400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr10:93862400-93867400	Weak transcription	K562	blood
16	chr10:93862400-93868800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr10:93862600-93870000	Weak transcription	NHLF	lung
18	chr10:93862800-93873200	Weak transcription	Fetal Muscle Leg	muscle
19	chr10:93863000-93870000	Weak transcription	Psoas Muscle	Psoas
20	chr10:93863000-93870200	Weak transcription	Primary T cells from cord blood	blood
21	chr10:93863000-93878600	Weak transcription	Gastric	stomach
22	chr10:93863200-93867400	Weak transcription	Aorta	Aorta
23	chr10:93863200-93869400	Weak transcription	Brain Substantia Nigra	brain
24	chr10:93863400-93867600	Enhancers	Liver	Liver
25	chr10:93863400-93870000	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr10:93863600-93869600	Weak transcription	HSMM	muscle
27	chr10:93863600-93870000	Weak transcription	Small Intestine	intestine
28	chr10:93863800-93869800	Weak transcription	Brain Anterior Caudate	brain
29	chr10:93863800-93879200	Weak transcription	GM12878-XiMat	blood
30	chr10:93863800-93881400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr10:93863800-93881600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr10:93864000-93869400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:93865600-93870200	Weak transcription	HepG2	liver
34	chr10:93866200-93869600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr10:93866600-93867800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr10:93866800-93867400	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr10:93866800-93867600	Enhancers	Fetal Heart	heart
38	chr10:93866800-93868000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr10:93866800-93869200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr10:93867000-93867400	Enhancers	HUVEC	blood vessel
41	chr10:93867000-93867600	Enhancers	Brain Hippocampus Middle	brain
42	chr10:93867000-93870600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr10:93867200-93867400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr10:93867200-93867400	Enhancers	Pancreas	Pancrea
45	chr10:93867200-93867400	Enhancers	Right Ventricle	heart
46	chr10:93867200-93867400	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr10:93867200-93867400	Enhancers	Stomach Mucosa	stomach
48	chr10:93867200-93867600	Enhancers	Brain Angular Gyrus	brain
49	chr10:93867200-93867600	Enhancers	Brain Cingulate Gyrus	brain
50	chr10:93867200-93868000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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