Variant report

Variant	rs7109648
Chromosome Location	chr11:9997065-9997066
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	chr11:9994842..9997807-chr11:10313418..10316499,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133812	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12098983	0.86[EUR][1000 genomes]
rs12274440	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17271623	0.86[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17272133	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17356369	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs61876942	0.83[EUR][1000 genomes]
rs61876945	0.83[EUR][1000 genomes]
rs61876948	0.83[EUR][1000 genomes]
rs61876949	0.86[EUR][1000 genomes]
rs61876951	0.88[EUR][1000 genomes]
rs61876972	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61876973	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61876974	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61876975	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61876976	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61876977	0.90[EUR][1000 genomes]
rs61876978	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61876980	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61876982	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61876983	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61876984	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61877004	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61877005	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61877038	0.85[EUR][1000 genomes]
rs61877039	0.86[EUR][1000 genomes]
rs61877046	0.84[EUR][1000 genomes]
rs6483859	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66536570	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66553354	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7108187	0.86[EUR][1000 genomes]
rs7110027	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7117364	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7118211	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7118427	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7120403	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7123546	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72854502	0.83[EUR][1000 genomes]
rs72855652	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72855680	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72857108	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7342224	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7935235	0.88[EUR][1000 genomes]
rs7936602	0.83[EUR][1000 genomes]
rs7938570	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7938773	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7945309	0.86[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs7949110	0.88[EUR][1000 genomes]
rs7949493	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7952455	0.86[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9666488	0.83[EUR][1000 genomes]

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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv896989	chr11:9951968-10059623	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv1819684	chr11:9973062-10012511	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7109648	RPL27A	cis	cerebellum	SCAN
rs7109648	OR5P3	cis	cerebellum	SCAN
rs7109648	ARFIP2	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9973800-10010600	Weak transcription	Fetal Brain Male	brain
2	chr11:9974200-9999000	Weak transcription	Fetal Heart	heart
3	chr11:9974200-9999000	Weak transcription	HSMMtube	muscle
4	chr11:9979800-9999200	Weak transcription	NH-A	brain
5	chr11:9981000-10020000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:9981200-10004200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:9981200-10009200	Weak transcription	Brain Germinal Matrix	brain
8	chr11:9981400-9999000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr11:9981400-10002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:9981400-10003400	Weak transcription	Brain Anterior Caudate	brain
11	chr11:9981400-10003400	Weak transcription	NHEK	skin
12	chr11:9981400-10003600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:9981400-10004200	Weak transcription	Esophagus	oesophagus
14	chr11:9981400-10004200	Weak transcription	Lung	lung
15	chr11:9981400-10004400	Weak transcription	HepG2	liver
16	chr11:9981400-10008800	Weak transcription	Primary T cells from cord blood	blood
17	chr11:9981400-10010200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr11:9981400-10014800	Weak transcription	Dnd41	blood
19	chr11:9981400-10017000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr11:9981400-10051600	Weak transcription	Aorta	Aorta
21	chr11:9981600-10003400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr11:9981800-10003400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:9981800-10004800	Weak transcription	Ovary	ovary
24	chr11:9983600-10004800	Weak transcription	Fetal Lung	lung
25	chr11:9983600-10023200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:9983800-9997200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr11:9984600-10010200	Weak transcription	Fetal Kidney	kidney
28	chr11:9984800-9999200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:9985000-9998000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:9985800-9997600	Weak transcription	Fetal Intestine Small	intestine
31	chr11:9985800-9998800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr11:9985800-10000600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr11:9985800-10004000	Weak transcription	Placenta	Placenta
34	chr11:9985800-10004200	Weak transcription	Fetal Muscle Leg	muscle
35	chr11:9985800-10004400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr11:9985800-10021600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:9985800-10023600	Weak transcription	Primary B cells from cord blood	blood
38	chr11:9985800-10049000	Weak transcription	Left Ventricle	heart
39	chr11:9986000-10006000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:9987200-10003600	Weak transcription	Hela-S3	cervix
41	chr11:9987600-10002600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:9989400-10004000	Weak transcription	Fetal Stomach	stomach
43	chr11:9990000-10002600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:9990000-10004800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr11:9990000-10012600	Weak transcription	Liver	Liver
46	chr11:9990000-10018200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr11:9990200-9998800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr11:9990200-10006200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr11:9990400-9998000	Weak transcription	Fetal Intestine Large	intestine
50	chr11:9990400-10028200	Weak transcription	Fetal Brain Female	brain

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