Variant report

Variant	rs2853066
Chromosome Location	chr11:75189157-75189158
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	chr11:75187397..75189556-chr11:75217050..75219601,2	K562	blood:

Variant related genes	Relation type
ENSG00000254460	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1004856	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11236441	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1540210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557471	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1631470	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1783559	1.00[JPT][hapmap]
rs1790144	1.00[JPT][hapmap]
rs1790147	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1790152	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793410	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1793414	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs499613	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504793	0.94[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];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511190	0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs514477	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540269	0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs544719	0.91[EUR][1000 genomes]
rs548439	0.92[EUR][1000 genomes]
rs549034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566818	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs571353	0.81[CEU][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs581007	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs589724	0.94[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];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs628972	1.00[CEU][hapmap];0.85[CHD][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs667410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669601	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs682292	0.94[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];0.90[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3381903	chr11:75123498-75587233	Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv897923	chr11:75129007-75302855	Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2853066	ARAP1	cis	cerebellum	SCAN
rs2853066	FLJ33790	cis	multi-tissue	Pritchard
rs2853066	UCP3	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75182400-75192400	Strong transcription	Fetal Intestine Large	intestine
2	chr11:75187000-75190000	Weak transcription	Fetal Stomach	stomach
3	chr11:75187000-75193600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:75187000-75194800	Strong transcription	Fetal Intestine Small	intestine
5	chr11:75187000-75201400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:75187200-75191000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr11:75187200-75201200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr11:75187200-75203000	Weak transcription	Primary T cells from cord blood	blood
9	chr11:75187400-75190600	Weak transcription	Right Atrium	heart
10	chr11:75187400-75191400	Weak transcription	GM12878-XiMat	blood
11	chr11:75187400-75192000	Weak transcription	Thymus	Thymus
12	chr11:75187400-75192200	Strong transcription	HepG2	liver
13	chr11:75187400-75198200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:75187400-75202800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr11:75187400-75202800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr11:75187400-75202800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:75187400-75203000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr11:75187600-75190000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr11:75187600-75192600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr11:75187600-75201000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:75187600-75202000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr11:75187800-75189200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr11:75187800-75189400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:75187800-75189400	Weak transcription	Fetal Brain Female	brain
25	chr11:75187800-75189800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr11:75187800-75190000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:75187800-75190000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:75187800-75192800	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr11:75187800-75201000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:75188000-75190000	Strong transcription	Adipose Nuclei	Adipose
31	chr11:75188000-75201600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr11:75188200-75200400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr11:75188400-75190000	Weak transcription	Left Ventricle	heart
34	chr11:75188400-75191000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:75188400-75191400	Weak transcription	Psoas Muscle	Psoas
36	chr11:75188400-75191400	Weak transcription	Right Ventricle	heart
37	chr11:75188400-75194000	Enhancers	Fetal Brain Male	brain
38	chr11:75188400-75201200	Weak transcription	HSMM	muscle
39	chr11:75188400-75201400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:75188400-75201400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:75188400-75201600	Weak transcription	HSMMtube	muscle
42	chr11:75188600-75193000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr11:75188600-75201600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr11:75188800-75189800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr11:75188800-75190000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr11:75188800-75190000	Weak transcription	K562	blood
47	chr11:75188800-75190200	Weak transcription	Liver	Liver
48	chr11:75188800-75190200	Strong transcription	Placenta	Placenta
49	chr11:75188800-75192200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr11:75188800-75192200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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