Variant report

Variant	rs4394802
Chromosome Location	chr11:46990587-46990588
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1007738	0.83[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs10501319	0.93[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs1060573	0.91[GIH][hapmap];0.87[MEX][hapmap]
rs10769211	0.83[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs10769225	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769226	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769227	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769228	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769234	0.82[CHB][hapmap]
rs10838635	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838640	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10838641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838644	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838646	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838652	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838658	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10838660	0.91[GIH][hapmap];0.83[MEX][hapmap]
rs10838662	0.93[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.81[ASN][1000 genomes]
rs10838663	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11039002	0.81[JPT][hapmap]
rs11039014	0.83[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs11039028	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039033	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11039035	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11039057	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039074	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs11039080	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11039081	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11039097	0.91[GIH][hapmap];0.82[MEX][hapmap]
rs11039105	0.91[GIH][hapmap];0.82[MEX][hapmap]
rs11039112	0.91[GIH][hapmap];0.82[MEX][hapmap]
rs11600292	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11601798	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11602250	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603373	0.80[ASN][1000 genomes]
rs11608083	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12417519	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.84[ASN][1000 genomes]
rs12574410	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12796744	0.94[GIH][hapmap];0.83[MEX][hapmap]
rs12807111	0.83[EUR][1000 genomes]
rs1551744	0.83[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs17790204	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1872896	0.91[GIH][hapmap];0.87[MEX][hapmap]
rs2035068	0.81[EUR][1000 genomes]
rs2087215	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs2279439	0.80[ASN][1000 genomes]
rs2306028	0.81[JPT][hapmap]
rs2306033	0.81[JPT][hapmap]
rs2306035	0.82[EUR][1000 genomes]
rs2306036	0.81[JPT][hapmap]
rs2306037	0.81[JPT][hapmap]
rs34340483	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3922684	0.84[ASN][1000 genomes]
rs4269876	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4294527	0.81[JPT][hapmap]
rs4315028	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4494268	0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4498951	0.84[ASN][1000 genomes]
rs4528282	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4548577	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4576779	0.83[ASN][1000 genomes]
rs4581406	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4587689	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs4752815	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752816	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752933	0.81[JPT][hapmap]
rs4752946	0.81[JPT][hapmap]
rs4752947	0.81[JPT][hapmap]
rs4752951	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752957	0.94[GIH][hapmap];0.87[MEX][hapmap]
rs4752965	0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4752969	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.81[ASN][1000 genomes]
rs61896133	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61896136	0.84[ASN][1000 genomes]
rs6485715	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6485716	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6485726	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6485739	0.91[GIH][hapmap];0.87[MEX][hapmap]
rs7101374	0.83[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs7103581	0.94[GIH][hapmap];0.87[MEX][hapmap]
rs7107778	0.85[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]
rs7108822	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7108902	0.94[GIH][hapmap];0.82[MEX][hapmap]
rs7111270	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7112854	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs7114683	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7121418	0.91[GIH][hapmap];0.87[MEX][hapmap]
rs7123632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7124648	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7125807	0.94[GIH][hapmap];0.86[MEX][hapmap]
rs7126005	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7127741	0.91[CEU][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7128193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7128650	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7130947	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs747650	0.91[GIH][hapmap];0.82[MEX][hapmap]
rs7929688	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7931260	0.94[GIH][hapmap];0.82[MEX][hapmap]
rs7935346	0.88[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7938169	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7939786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7940240	0.80[ASN][1000 genomes]
rs7940441	0.81[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7945315	0.94[GIH][hapmap];0.87[MEX][hapmap]
rs7945558	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7946709	0.94[GIH][hapmap];0.83[MEX][hapmap]
rs7946739	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7950753	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs923324	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs964551	0.85[GIH][hapmap];0.81[JPT][hapmap];0.93[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1805201	chr11:46971012-47063429	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv1819852	chr11:46971012-47064542	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4394802	NUP160	cis	cerebellum	SCAN
rs4394802	ACP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46959000-46998600	Weak transcription	Left Ventricle	heart
2	chr11:46959200-46990600	Weak transcription	Brain Angular Gyrus	brain
3	chr11:46959200-46990600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:46959200-46993800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr11:46970600-46993200	Weak transcription	Small Intestine	intestine
6	chr11:46971000-46992400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:46971600-46995600	Weak transcription	Pancreas	Pancrea
8	chr11:46971600-47006600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr11:46974200-46998600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:46974200-47008400	Weak transcription	Primary T cells from cord blood	blood
11	chr11:46980400-46998600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:46980400-46998600	Weak transcription	Thymus	Thymus
13	chr11:46980600-46990600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:46980600-46992600	Weak transcription	Fetal Lung	lung
15	chr11:46980600-46995400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:46980600-46995400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:46980600-46995400	Weak transcription	Fetal Stomach	stomach
18	chr11:46980600-46998600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:46980600-46999600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:46980600-47014000	Weak transcription	Aorta	Aorta
21	chr11:46980600-47021000	Weak transcription	Ovary	ovary
22	chr11:46980600-47026000	Weak transcription	HSMM	muscle
23	chr11:46981200-47023400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr11:46981400-46997400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:46982600-46997000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:46982800-46993200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:46982800-46998400	Weak transcription	Fetal Brain Female	brain
28	chr11:46983000-46993400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:46983000-46993800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr11:46983000-46997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:46983000-47024000	Weak transcription	Primary B cells from cord blood	blood
32	chr11:46983200-46993400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr11:46983400-46998600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:46984000-46997000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:46985000-46997400	Weak transcription	GM12878-XiMat	blood
36	chr11:46986400-46993800	Weak transcription	Fetal Intestine Small	intestine
37	chr11:46986600-46994800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:46986600-46995600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:46986600-46997400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:46987600-46991000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:46988400-46991000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:46988400-46992800	Strong transcription	Hela-S3	cervix
43	chr11:46988400-46995000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr11:46988600-46997800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr11:46989200-47026000	Weak transcription	Dnd41	blood
46	chr11:46989800-46998400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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