Variant report

Variant	rs10840385
Chromosome Location	chr11:10307636-10307637
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10288226..10290717-chr11:10306819..10308555,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10500721	0.84[ASN][1000 genomes]
rs10500722	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10500724	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10743131	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10743133	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10770104	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10770105	0.93[ASN][1000 genomes]
rs10840380	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10840381	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840382	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840384	0.80[ASN][1000 genomes]
rs11042662	0.84[ASN][1000 genomes]
rs11042687	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042702	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042703	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042712	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11042714	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11042716	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11042717	0.86[ASN][1000 genomes]
rs11042719	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11602090	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11607174	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12279861	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12290748	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12419064	0.84[ASN][1000 genomes]
rs12419593	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1442738	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2044143	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2044144	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2060658	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2083715	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2083716	0.85[EUR][1000 genomes]
rs2083717	0.84[ASN][1000 genomes]
rs2278634	0.83[ASN][1000 genomes]
rs2920147	0.86[ASN][1000 genomes]
rs34051776	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34087225	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34692066	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34739790	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35737881	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35752075	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36167833	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36170347	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4267063	0.84[ASN][1000 genomes]
rs4323860	0.83[ASN][1000 genomes]
rs4418806	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4442543	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4482025	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4491213	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4597056	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4910107	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4910108	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4910115	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55893317	0.81[ASN][1000 genomes]
rs55933041	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56063978	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56758314	0.82[ASN][1000 genomes]
rs56776911	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61889955	0.82[ASN][1000 genomes]
rs6484141	0.80[EUR][1000 genomes]
rs6484147	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6484148	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6484152	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6484160	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7106998	0.82[EUR][1000 genomes]
rs7107040	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7107290	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7107399	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7107951	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7108358	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7110652	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7115142	0.82[ASN][1000 genomes]
rs7115944	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7116147	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7118500	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7123728	0.83[ASN][1000 genomes]
rs716803	0.91[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs726102	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7479039	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7924631	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7938543	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7945930	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7947666	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7950461	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7952105	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9735682	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10840385	RP11-351I24.1	cis	Whole Blood	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10278200-10309200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:10279000-10311400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr11:10290000-10313400	Weak transcription	Fetal Brain Male	brain
4	chr11:10290800-10309000	Weak transcription	HSMMtube	muscle
5	chr11:10291200-10313600	Weak transcription	NHEK	skin
6	chr11:10291200-10314400	Weak transcription	HSMM	muscle
7	chr11:10291400-10309000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr11:10294200-10309600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:10294200-10311400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:10297000-10309600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr11:10297800-10309400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:10298200-10313400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:10299400-10308600	Weak transcription	NHLF	lung
14	chr11:10299400-10314800	Weak transcription	Small Intestine	intestine
15	chr11:10299600-10310400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:10299800-10314400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr11:10304000-10312400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr11:10304800-10308800	Weak transcription	Fetal Intestine Large	intestine
19	chr11:10304800-10308800	Weak transcription	Fetal Intestine Small	intestine
20	chr11:10304800-10308800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:10305000-10308400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr11:10305800-10307800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr11:10306000-10307800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:10306000-10307800	Enhancers	HepG2	liver
25	chr11:10306200-10307800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:10306200-10307800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr11:10306200-10309400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:10306400-10309000	Weak transcription	Right Ventricle	heart
29	chr11:10306400-10313800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr11:10306600-10314400	Weak transcription	Brain Germinal Matrix	brain
31	chr11:10306600-10314800	Weak transcription	Aorta	Aorta
32	chr11:10306800-10308000	Enhancers	Hela-S3	cervix
33	chr11:10306800-10309200	Weak transcription	Lung	lung
34	chr11:10306800-10309400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:10306800-10309400	Weak transcription	Esophagus	oesophagus
36	chr11:10306800-10309400	Weak transcription	Placenta	Placenta
37	chr11:10306800-10309400	Weak transcription	Spleen	Spleen
38	chr11:10306800-10311000	Weak transcription	Ovary	ovary
39	chr11:10307000-10307800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr11:10307000-10307800	Enhancers	Liver	Liver
41	chr11:10307000-10308800	Weak transcription	Right Atrium	heart
42	chr11:10307000-10309000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr11:10307000-10309000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:10307000-10309200	Weak transcription	Fetal Stomach	stomach
45	chr11:10307000-10309400	Weak transcription	Gastric	stomach
46	chr11:10307000-10309600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr11:10307000-10313800	Weak transcription	Psoas Muscle	Psoas
48	chr11:10307000-10314400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:10307200-10313400	Weak transcription	Fetal Kidney	kidney
50	chr11:10307200-10313400	Weak transcription	HUVEC	blood vessel

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