Variant report

Variant	rs684546
Chromosome Location	chr11:65782622-65782623
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65780273..65782876-chr11:65822009..65824161,2	K562	blood:
2	chr11:65780649..65783922-chr11:65810860..65813653,4	MCF-7	breast:
3	chr11:65781018..65783693-chr11:66000145..66002258,2	K562	blood:
4	chr11:65780378..65783041-chr11:65792155..65793993,2	MCF-7	breast:
5	chr11:65780844..65784041-chr11:65834496..65838705,4	MCF-7	breast:
6	chr11:65781033..65783841-chr11:65908931..65911172,2	MCF-7	breast:
7	chr11:65654636..65658395-chr11:65779993..65782935,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172500	Chromatin interaction
ENSG00000175229	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000175115	Chromatin interaction
ENSG00000255038	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175294	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11227378	0.88[AMR][1000 genomes]
rs1151510	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1151511	0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs1151514	0.85[GIH][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1191716	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1192184	0.82[EUR][1000 genomes]
rs1204011	0.83[EUR][1000 genomes]
rs1786171	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1786172	0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1786174	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs502363	0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs506873	0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs507672	0.85[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs522553	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs534201	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs540584	0.82[EUR][1000 genomes]
rs543952	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs548435	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs548495	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs549334	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs559161	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs586921	0.85[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs590531	0.83[EUR][1000 genomes]
rs610497	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs615646	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs619701	0.83[EUR][1000 genomes]
rs622779	0.85[GIH][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs632640	0.94[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs645571	0.83[EUR][1000 genomes]
rs668210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs677350	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs685334	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7933510	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
2	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	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
4	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv897769	chr11:65727799-65828625	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs684546	SNORD26	cis	parietal	SCAN
rs684546	MRPL11	cis	cerebellum	SCAN
rs684546	KAT5	cis	cerebellum	SCAN
rs684546	SNX32	cis	parietal	SCAN
rs684546	RTN3	cis	parietal	SCAN
rs684546	DKFZp761E198	cis	cerebellum	SCAN
rs684546	TCIRG1	cis	parietal	SCAN
rs684546	ESRRA	cis	cerebellum	SCAN
rs684546	PC	cis	parietal	SCAN
rs684546	NDUFV1	cis	cerebellum	SCAN
rs684546	POLR2G	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65779800-65783200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr11:65780600-65783400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr11:65780800-65782800	Weak transcription	Aorta	Aorta
4	chr11:65780800-65784000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:65780800-65788600	Weak transcription	NHEK	skin
6	chr11:65781000-65782800	Weak transcription	Right Ventricle	heart
7	chr11:65781200-65787600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:65781200-65788200	Weak transcription	Esophagus	oesophagus
9	chr11:65781400-65787200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:65781600-65782800	Weak transcription	Placenta	Placenta
11	chr11:65781600-65783600	Weak transcription	K562	blood
12	chr11:65782000-65783400	Enhancers	HSMMtube	muscle
13	chr11:65782200-65782800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:65782200-65782800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr11:65782200-65783000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:65782200-65783800	Enhancers	Spleen	Spleen
17	chr11:65782200-65784200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr11:65782200-65784200	Flanking Active TSS	Hela-S3	cervix
19	chr11:65782200-65784200	Enhancers	HMEC	breast
20	chr11:65782200-65784200	Enhancers	HUVEC	blood vessel
21	chr11:65782200-65784400	Enhancers	NHDF-Ad	bronchial
22	chr11:65782400-65782800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr11:65782400-65783200	Enhancers	Osteobl	bone
24	chr11:65782400-65783400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:65782400-65783800	Enhancers	NH-A	brain
26	chr11:65782400-65784000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:65782400-65784200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:65782400-65784200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:65782400-65784200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:65782400-65784200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:65782400-65784400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
32	chr11:65782400-65784400	Enhancers	Fetal Heart	heart
33	chr11:65782400-65784600	Enhancers	Fetal Muscle Leg	muscle
34	chr11:65782600-65783200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr11:65782600-65783200	Enhancers	Psoas Muscle	Psoas
36	chr11:65782600-65783400	Enhancers	Left Ventricle	heart
37	chr11:65782600-65783400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr11:65782600-65783400	Enhancers	A549	lung
39	chr11:65782600-65783600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr11:65782600-65783600	Enhancers	Lung	lung
41	chr11:65782600-65783800	Enhancers	Right Atrium	heart
42	chr11:65782600-65784000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:65782600-65784400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:65782600-65784400	Enhancers	Fetal Muscle Trunk	muscle
45	chr11:65782600-65784600	Flanking Active TSS	HSMM	muscle
46	chr11:65782600-65789800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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