Variant report

Variant	rs11042064
Chromosome Location	chr11:8799749-8799750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr11:8799510-8799959	GM12878	blood:	n/a	chr11:8799831-8799849
2	SPI1	chr11:8799597-8799948	GM12878	blood:	n/a	chr11:8799825-8799834
3	SPI1	chr11:8799715-8799901	GM12878	blood:	n/a	chr11:8799825-8799834
4	BCL11A	chr11:8799642-8799949	GM12878	blood:	n/a	n/a
5	SPI1	chr11:8799390-8800161	GM12878	blood:	n/a	chr11:8799825-8799834
6	SPI1	chr11:8799580-8800023	GM12891	blood:	n/a	chr11:8799825-8799834
7	SPI1	chr11:8799560-8799957	GM12891	blood:	n/a	chr11:8799825-8799834
8	MXI1	chr11:8799282-8800459	IMR90	lung:	n/a	n/a
9	MTA3	chr11:8799496-8800065	GM12878	blood:	n/a	n/a
10	NFYB	chr11:8799709-8799854	GM12878	blood:	n/a	n/a
11	RUNX3	chr11:8799529-8800005	GM12878	blood:	n/a	n/a
12	EP300	chr11:8799686-8799947	GM12878	blood:	n/a	chr11:8799825-8799839

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:8799185..8801776-chr11:8804867..8806861,2	K562	blood:
2	chr11:8708821..8711720-chr11:8797773..8800794,3	MCF-7	breast:

Variant related genes	Relation type
ST5	TF binding region
ENSG00000166441	Chromatin interaction
ENSG00000255159	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10743086	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10743090	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10769961	0.83[CEU][hapmap]
rs10840119	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10840120	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840122	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10840124	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11042052	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs11042074	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12269980	0.85[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs12287694	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12289240	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12291552	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12420964	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16906037	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2316863	0.83[CEU][hapmap]
rs3763917	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3763919	0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs3913547	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4082668	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4370937	0.88[CEU][hapmap]
rs4929918	0.83[CEU][hapmap]
rs55902154	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60869409	0.85[EUR][1000 genomes]
rs61875931	0.87[EUR][1000 genomes]
rs6484007	0.94[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs6484606	0.88[CEU][hapmap]
rs7105372	0.94[CEU][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7131166	0.88[CEU][hapmap]
rs72858278	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758256	chr11:8784813-9009573	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv2759803	chr11:8784813-9009573	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv553447	chr11:8792622-8825966	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11042064	OR51M1	cis	parietal	SCAN
rs11042064	RPL27A	cis	cerebellum	SCAN
rs11042064	PPFIBP2	cis	parietal	SCAN
rs11042064	DNHD1	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8786600-8803000	Enhancers	Ovary	ovary
2	chr11:8788800-8801400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:8788800-8808400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:8789000-8801200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:8789400-8807600	Weak transcription	Fetal Kidney	kidney
6	chr11:8789600-8805800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:8791400-8810400	Weak transcription	Hela-S3	cervix
8	chr11:8792600-8802400	Genic enhancers	Fetal Stomach	stomach
9	chr11:8793200-8801600	Genic enhancers	Fetal Muscle Leg	muscle
10	chr11:8794200-8801000	Enhancers	Pancreas	Pancrea
11	chr11:8794200-8803000	Enhancers	Left Ventricle	heart
12	chr11:8794600-8803000	Enhancers	Right Ventricle	heart
13	chr11:8795000-8801400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr11:8795000-8809800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:8795600-8802600	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr11:8796200-8801200	Enhancers	HSMMtube	muscle
17	chr11:8796200-8808000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:8796400-8800000	Weak transcription	Fetal Thymus	thymus
19	chr11:8796800-8800000	Weak transcription	Colonic Mucosa	Colon
20	chr11:8796800-8801000	Genic enhancers	HSMM	muscle
21	chr11:8797000-8801000	Enhancers	Psoas Muscle	Psoas
22	chr11:8797000-8801200	Enhancers	Aorta	Aorta
23	chr11:8797400-8800000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:8797400-8801800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:8797400-8808200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr11:8797800-8801800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr11:8797800-8827200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:8798000-8800000	Weak transcription	Placenta	Placenta
29	chr11:8798000-8800000	Strong transcription	NHEK	skin
30	chr11:8798000-8800800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr11:8798200-8799800	Weak transcription	HMEC	breast
32	chr11:8798200-8800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:8798200-8800000	Enhancers	Colon Smooth Muscle	Colon
34	chr11:8798200-8800600	Weak transcription	HepG2	liver
35	chr11:8798200-8808200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:8798200-8808400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr11:8798200-8810000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:8798400-8803200	Strong transcription	Liver	Liver
39	chr11:8798600-8800000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr11:8798600-8807400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr11:8798800-8800200	Enhancers	GM12878-XiMat	blood
42	chr11:8798800-8801200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:8799000-8800200	Enhancers	NHLF	lung
44	chr11:8799000-8801600	Enhancers	Stomach Mucosa	stomach
45	chr11:8799200-8800000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:8799200-8800200	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr11:8799200-8801000	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr11:8799200-8801000	Genic enhancers	NHDF-Ad	bronchial
49	chr11:8799200-8801400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:8799400-8799800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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