Variant report

Variant	rs539046
Chromosome Location	chr11:65843778-65843779
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65822840..65824603-chr11:65843148..65845154,2	MCF-7	breast:
2	chr11:65818986..65821722-chr11:65843087..65845750,3	K562	blood:
3	chr11:65842058..65844229-chr11:65885606..65887262,2	MCF-7	breast:
4	chr11:65837300..65840343-chr11:65840812..65845835,6	K562	blood:
5	chr11:65843731..65845242-chr11:65847002..65849986,2	K562	blood:
6	chr11:65818921..65820486-chr11:65841745..65844587,2	K562	blood:
7	chr11:65810450..65813248-chr11:65842364..65844217,2	K562	blood:

Variant related genes	Relation type
ENSG00000175115	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175229	Chromatin interaction
ENSG00000238752	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1151530	0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1642958	0.92[AMR][1000 genomes]
rs2241303	0.82[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes]
rs2430978	0.84[AMR][1000 genomes]
rs2576	0.83[ASW][hapmap];0.81[CEU][hapmap];0.83[YRI][hapmap]
rs2845570	0.83[ASW][hapmap];0.83[YRI][hapmap]
rs472518	0.81[GIH][hapmap]
rs482414	0.89[ASN][1000 genomes]
rs484983	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs486311	0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs493320	0.90[AMR][1000 genomes]
rs524281	0.81[GIH][hapmap]
rs526852	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs527737	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs527897	0.81[GIH][hapmap]
rs527962	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs537497	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs564343	0.92[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs570760	0.82[AMR][1000 genomes]
rs571374	0.82[CEU][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.91[AMR][1000 genomes]
rs576740	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576836	0.81[CEU][hapmap];0.92[AMR][1000 genomes]
rs577013	0.92[AMR][1000 genomes]
rs801741	0.89[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
3	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs539046	RP11-867O8.5	cis	Artery Aorta	GTEx
rs539046	SF3B2	cis	parietal	SCAN
rs539046	SF3B2	cis	cerebellum	SCAN
rs539046	SLC22A6	cis	cerebellum	SCAN
rs539046	TBC1D10C	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65839000-65849800	Weak transcription	Psoas Muscle	Psoas
2	chr11:65839200-65843800	Weak transcription	Esophagus	oesophagus
3	chr11:65839200-65843800	Weak transcription	Pancreas	Pancrea
4	chr11:65839200-65844200	Weak transcription	Aorta	Aorta
5	chr11:65839200-65846800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:65839200-65847600	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:65839200-65847800	Weak transcription	Colonic Mucosa	Colon
8	chr11:65839400-65847200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr11:65839400-65847200	Weak transcription	Right Atrium	heart
10	chr11:65839400-65847600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:65839400-65847600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr11:65839400-65847600	Weak transcription	Small Intestine	intestine
13	chr11:65839400-65847800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:65839400-65848800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:65839400-65850400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:65839400-65850400	Weak transcription	Fetal Intestine Large	intestine
17	chr11:65839400-65850800	Weak transcription	Liver	Liver
18	chr11:65839400-65850800	Weak transcription	Fetal Kidney	kidney
19	chr11:65839400-65850800	Weak transcription	Right Ventricle	heart
20	chr11:65839600-65844000	Weak transcription	HMEC	breast
21	chr11:65839600-65850400	Weak transcription	Brain Substantia Nigra	brain
22	chr11:65839600-65854600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr11:65839800-65845200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr11:65840000-65844200	Weak transcription	NHDF-Ad	bronchial
25	chr11:65840000-65844800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr11:65840000-65846600	Strong transcription	Fetal Muscle Leg	muscle
27	chr11:65840000-65847400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr11:65840000-65847600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr11:65840000-65847600	Weak transcription	Colon Smooth Muscle	Colon
30	chr11:65840200-65844000	Weak transcription	Thymus	Thymus
31	chr11:65840200-65844200	Weak transcription	NHLF	lung
32	chr11:65840200-65846200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
33	chr11:65840200-65848000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr11:65840200-65848200	Strong transcription	Fetal Stomach	stomach
35	chr11:65840400-65844000	Weak transcription	Gastric	stomach
36	chr11:65840400-65844400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:65840400-65844600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr11:65840400-65845000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:65840400-65845400	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr11:65840400-65847600	Weak transcription	HUVEC	blood vessel
41	chr11:65840600-65844200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr11:65840600-65844400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr11:65840600-65844400	Weak transcription	K562	blood
44	chr11:65840600-65845800	Strong transcription	Fetal Thymus	thymus
45	chr11:65840600-65850800	Weak transcription	Brain Germinal Matrix	brain
46	chr11:65840600-65870600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr11:65840800-65844000	Weak transcription	Spleen	Spleen
48	chr11:65840800-65844200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:65840800-65847200	Weak transcription	Lung	lung
50	chr11:65840800-65850400	Weak transcription	Fetal Brain Male	brain

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