Variant report

Variant	rs7107399
Chromosome Location	chr11:10294887-10294888
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10293712..10297432-chr11:10324720..10326890,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254554	Chromatin interaction
ENSG00000148926	Chromatin interaction

Extended variants
information (count: 171 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10500720	0.80[ASN][1000 genomes]
rs10500721	0.89[ASN][1000 genomes]
rs10500722	0.94[ASN][1000 genomes]
rs10500723	0.80[ASN][1000 genomes]
rs10500724	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10743131	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10743132	0.86[ASN][1000 genomes]
rs10743133	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10770104	0.90[EUR][1000 genomes]
rs10770105	0.95[ASN][1000 genomes]
rs10840379	0.86[ASN][1000 genomes]
rs10840380	0.89[EUR][1000 genomes]
rs10840381	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840382	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840384	0.85[ASN][1000 genomes]
rs10840385	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10840386	0.81[ASN][1000 genomes]
rs11042652	0.81[ASN][1000 genomes]
rs11042653	0.81[ASN][1000 genomes]
rs11042656	0.82[ASN][1000 genomes]
rs11042657	0.82[ASN][1000 genomes]
rs11042659	0.82[ASN][1000 genomes]
rs11042661	0.82[ASN][1000 genomes]
rs11042662	0.89[ASN][1000 genomes]
rs11042663	0.82[ASN][1000 genomes]
rs11042664	0.82[ASN][1000 genomes]
rs11042666	0.83[ASN][1000 genomes]
rs11042686	0.85[ASN][1000 genomes]
rs11042687	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042689	0.86[ASN][1000 genomes]
rs11042702	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042703	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042712	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11042714	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042716	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11042717	0.88[ASN][1000 genomes]
rs11042719	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11602090	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11607174	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11607621	0.86[ASN][1000 genomes]
rs11821308	0.85[ASN][1000 genomes]
rs12274104	0.81[ASN][1000 genomes]
rs12275224	0.82[ASN][1000 genomes]
rs12278680	0.84[ASN][1000 genomes]
rs12278735	0.81[ASN][1000 genomes]
rs12279861	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12280005	0.83[ASN][1000 genomes]
rs12281409	0.84[ASN][1000 genomes]
rs12281526	0.82[ASN][1000 genomes]
rs12282974	0.84[ASN][1000 genomes]
rs12284884	0.82[ASN][1000 genomes]
rs12286545	0.84[ASN][1000 genomes]
rs12286927	0.81[ASN][1000 genomes]
rs12287386	0.81[ASN][1000 genomes]
rs12288200	0.82[ASN][1000 genomes]
rs12288275	0.82[ASN][1000 genomes]
rs12288486	0.81[ASN][1000 genomes]
rs12288654	0.82[ASN][1000 genomes]
rs12290748	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12291196	0.81[ASN][1000 genomes]
rs12291198	0.81[ASN][1000 genomes]
rs12418690	0.86[ASN][1000 genomes]
rs12419064	0.85[ASN][1000 genomes]
rs12419593	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12421666	0.85[ASN][1000 genomes]
rs1442733	0.82[ASN][1000 genomes]
rs1442734	0.81[ASN][1000 genomes]
rs1442736	0.82[ASN][1000 genomes]
rs1442738	0.88[EUR][1000 genomes]
rs16907544	0.81[ASN][1000 genomes]
rs16907552	0.81[ASN][1000 genomes]
rs16907554	0.81[ASN][1000 genomes]
rs16907561	0.82[ASN][1000 genomes]
rs16907564	0.82[ASN][1000 genomes]
rs16907568	0.82[ASN][1000 genomes]
rs16907575	0.84[ASN][1000 genomes]
rs16907615	0.86[ASN][1000 genomes]
rs16907635	0.84[ASN][1000 genomes]
rs1812853	0.81[ASN][1000 genomes]
rs1822294	0.84[ASN][1000 genomes]
rs1822295	0.84[ASN][1000 genomes]
rs1867136	0.83[ASN][1000 genomes]
rs1867137	0.83[ASN][1000 genomes]
rs1867138	0.83[ASN][1000 genomes]
rs2044143	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2044144	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2060658	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2069214	0.81[ASN][1000 genomes]
rs2083715	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2083716	0.88[EUR][1000 genomes]
rs2083717	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2119991	0.83[ASN][1000 genomes]
rs2278634	0.85[ASN][1000 genomes]
rs2920147	0.93[ASN][1000 genomes]
rs2957671	0.86[ASN][1000 genomes]
rs2957674	0.86[ASN][1000 genomes]
rs2957699	0.86[ASN][1000 genomes]
rs34051776	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34087225	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34692066	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34739790	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35598338	0.86[ASN][1000 genomes]
rs35737881	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35752075	0.83[ASN][1000 genomes]
rs36167833	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36170347	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4267063	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4323860	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4418806	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4442543	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4482025	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4491213	0.82[ASN][1000 genomes]
rs4597056	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4910097	0.82[EUR][1000 genomes]
rs4910107	0.88[EUR][1000 genomes]
rs4910108	0.89[EUR][1000 genomes]
rs4910115	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55893317	0.86[ASN][1000 genomes]
rs55933041	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56063978	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56319831	0.85[ASN][1000 genomes]
rs56758314	0.87[ASN][1000 genomes]
rs56776911	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57153895	0.80[ASN][1000 genomes]
rs57521137	0.81[ASN][1000 genomes]
rs57522724	0.81[ASN][1000 genomes]
rs57595438	0.82[ASN][1000 genomes]
rs57761181	0.85[ASN][1000 genomes]
rs58054521	0.85[ASN][1000 genomes]
rs58340019	0.84[ASN][1000 genomes]
rs59829967	0.83[ASN][1000 genomes]
rs59901009	0.85[ASN][1000 genomes]
rs60319025	0.82[ASN][1000 genomes]
rs61877260	0.85[ASN][1000 genomes]
rs61878638	0.85[ASN][1000 genomes]
rs61889798	0.86[ASN][1000 genomes]
rs61889955	0.88[ASN][1000 genomes]
rs6484147	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6484148	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6484152	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6484160	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7106998	0.86[EUR][1000 genomes]
rs7107040	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7107290	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7107951	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7108358	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7110652	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7111724	0.82[ASN][1000 genomes]
rs7115142	0.85[ASN][1000 genomes]
rs7115944	0.88[EUR][1000 genomes]
rs7116147	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7118500	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7123728	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7129531	0.85[ASN][1000 genomes]
rs716803	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs726102	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7479039	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7924631	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7927874	0.80[ASN][1000 genomes]
rs7933018	0.86[ASN][1000 genomes]
rs7938543	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7945930	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7947666	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7950461	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7952105	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7952229	0.85[ASN][1000 genomes]
rs9735682	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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	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
2	esv3468808	chr11:10291076-10295774	Weak transcription Flanking Active TSS Enhancers Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
3	esv3499249	chr11:10291626-10294924	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
4	esv3443412	chr11:10293286-10294899	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7107399	RP11-351I24.1	cis	Whole Blood	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10268600-10300000	Weak transcription	Fetal Intestine Small	intestine
2	chr11:10278200-10295200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:10278200-10309200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:10279000-10311400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr11:10279400-10296600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:10281200-10295000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:10285400-10303400	Weak transcription	Fetal Intestine Large	intestine
8	chr11:10287600-10306200	Weak transcription	Psoas Muscle	Psoas
9	chr11:10287800-10295400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:10288000-10295000	Weak transcription	Ovary	ovary
11	chr11:10289200-10299200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:10289400-10299200	Weak transcription	Small Intestine	intestine
13	chr11:10290000-10313400	Weak transcription	Fetal Brain Male	brain
14	chr11:10290800-10309000	Weak transcription	HSMMtube	muscle
15	chr11:10291000-10295000	Weak transcription	NHDF-Ad	bronchial
16	chr11:10291200-10295000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:10291200-10295000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:10291200-10313600	Weak transcription	NHEK	skin
19	chr11:10291200-10314400	Weak transcription	HSMM	muscle
20	chr11:10291400-10295200	Weak transcription	NHLF	lung
21	chr11:10291400-10295200	Weak transcription	Osteobl	bone
22	chr11:10291400-10296000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr11:10291400-10296400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:10291400-10309000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:10294000-10295000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:10294000-10295000	Weak transcription	A549	lung
27	chr11:10294200-10295200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:10294200-10295200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:10294200-10298400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:10294200-10309600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:10294200-10311400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:10294800-10295600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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