Variant report

Variant	rs589724
Chromosome Location	chr11:75199181-75199182
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	chr11:75196940..75199795-chr11:75215143..75217908,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1004856	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs11236441	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1540210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557471	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1631470	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1783559	1.00[JPT][hapmap];0.80[YRI][hapmap]
rs1790144	1.00[JPT][hapmap]
rs1790147	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1790152	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1793410	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1793414	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2853066	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]
rs499613	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504793	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511190	0.83[EUR][1000 genomes]
rs514477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540269	0.82[EUR][1000 genomes]
rs544719	0.88[EUR][1000 genomes]
rs548439	0.89[EUR][1000 genomes]
rs549034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566818	0.83[EUR][1000 genomes]
rs571353	0.81[CEU][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs581007	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs628972	1.00[CEU][hapmap];0.85[CHD][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs667410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669601	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs682292	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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
3	nsv825996	chr11:75195626-75203332	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2757452	chr11:75198280-75201091	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv2759838	chr11:75198280-75201091	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs589724	ARAP1	cis	cerebellum	SCAN
rs589724	MYO7A	cis	parietal	SCAN
rs589724	UCP3	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:75187000-75201400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:75187200-75201200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr11:75187200-75203000	Weak transcription	Primary T cells from cord blood	blood
4	chr11:75187400-75202800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:75187400-75202800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:75187400-75202800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:75187400-75203000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr11:75187600-75201000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:75187600-75202000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:75187800-75201000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:75188000-75201600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr11:75188200-75200400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:75188400-75201200	Weak transcription	HSMM	muscle
14	chr11:75188400-75201400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr11:75188400-75201400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:75188400-75201600	Weak transcription	HSMMtube	muscle
17	chr11:75188600-75201600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr11:75190400-75199200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:75190400-75207400	Weak transcription	Fetal Stomach	stomach
20	chr11:75190800-75201600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:75192200-75202800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr11:75193000-75203200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr11:75193800-75203200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr11:75194000-75203000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr11:75194600-75203000	Weak transcription	Lung	lung
26	chr11:75195000-75201200	Weak transcription	Spleen	Spleen
27	chr11:75196400-75202200	Strong transcription	Fetal Intestine Small	intestine
28	chr11:75197800-75201400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr11:75197800-75201600	Enhancers	Brain Germinal Matrix	brain
30	chr11:75198000-75201000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr11:75198200-75201400	Strong transcription	Fetal Intestine Large	intestine
32	chr11:75198200-75203000	Weak transcription	Hela-S3	cervix
33	chr11:75198400-75201200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:75198400-75201200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:75198600-75199400	Enhancers	Adipose Nuclei	Adipose
36	chr11:75198600-75203600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr11:75198800-75200400	Strong transcription	Placenta	Placenta
38	chr11:75199000-75200000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr11:75199000-75201200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr11:75199000-75201200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr11:75199000-75201800	Strong transcription	HepG2	liver

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