Variant report

Variant	rs3802890
Chromosome Location	chr11:46534546-46534547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46524118..46526441-chr11:46533359..46535201,2	K562	blood:
2	chr11:46524483..46527091-chr11:46533404..46536130,2	MCF-7	breast:
3	chr11:46530140..46532187-chr11:46533691..46535503,2	K562	blood:
4	chr11:46411793..46414302-chr11:46533224..46536085,2	K562	blood:
5	chr11:46533516..46535465-chr11:46539167..46541545,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10769204	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10838596	0.88[CEU][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap]
rs10838601	0.81[EUR][1000 genomes]
rs10838610	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10838613	0.81[JPT][hapmap]
rs11038866	1.00[CEU][hapmap]
rs11038871	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11038910	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574259	0.81[JPT][hapmap]
rs1317826	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs17787804	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3740973	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752926	1.00[ASW][hapmap];0.91[LWK][hapmap];0.95[MKK][hapmap];0.82[YRI][hapmap]
rs61882719	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6485686	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs68002803	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7476	0.83[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap]
rs7484125	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7925678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7926389	0.81[JPT][hapmap]
rs7949282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7949371	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]

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	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046990	chr11:46501436-46669636	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv541031	chr11:46501436-46669636	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv897321	chr11:46515902-46673344	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3802890	TP53I11	cis	parietal	SCAN
rs3802890	OR4X2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46497600-46537600	Weak transcription	A549	lung
2	chr11:46503400-46563000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:46509600-46537200	Strong transcription	Primary T cells from cord blood	blood
4	chr11:46514200-46535000	Weak transcription	Small Intestine	intestine
5	chr11:46515000-46535000	Weak transcription	HUVEC	blood vessel
6	chr11:46515800-46537600	Weak transcription	NHDF-Ad	bronchial
7	chr11:46517200-46550000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:46522600-46534600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr11:46527000-46535000	Weak transcription	HMEC	breast
10	chr11:46527600-46537400	Weak transcription	NH-A	brain
11	chr11:46527800-46535200	Weak transcription	Pancreas	Pancrea
12	chr11:46527800-46535400	Weak transcription	Psoas Muscle	Psoas
13	chr11:46528000-46537400	Weak transcription	Osteobl	bone
14	chr11:46528200-46535000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:46529200-46534600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:46529600-46537400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr11:46529800-46535000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:46529800-46542400	Weak transcription	NHLF	lung
19	chr11:46529800-46542600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:46530000-46534600	Weak transcription	Fetal Brain Female	brain
21	chr11:46530000-46535000	Weak transcription	Brain Substantia Nigra	brain
22	chr11:46530000-46535200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr11:46530000-46535200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:46530000-46535200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:46530000-46535600	Weak transcription	Brain Angular Gyrus	brain
26	chr11:46530000-46535600	Weak transcription	Brain Anterior Caudate	brain
27	chr11:46530000-46535600	Weak transcription	Esophagus	oesophagus
28	chr11:46530000-46535600	Weak transcription	Right Ventricle	heart
29	chr11:46530000-46537600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:46530000-46540600	Weak transcription	Gastric	stomach
31	chr11:46530000-46542200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:46530000-46542600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:46530200-46535000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr11:46530200-46535200	Weak transcription	Brain Germinal Matrix	brain
35	chr11:46530200-46535200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr11:46530200-46535200	Weak transcription	Fetal Stomach	stomach
37	chr11:46530200-46535200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:46530200-46535600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr11:46530200-46535600	Weak transcription	Fetal Lung	lung
40	chr11:46530200-46535600	Weak transcription	GM12878-XiMat	blood
41	chr11:46530200-46537400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr11:46530200-46537400	Weak transcription	HSMM	muscle
43	chr11:46530200-46542400	Weak transcription	Hela-S3	cervix
44	chr11:46530200-46544200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:46530200-46550200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:46530200-46550600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr11:46530400-46535000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr11:46530400-46535000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr11:46530400-46535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr11:46530400-46535200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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