Variant report

Variant	rs10840380
Chromosome Location	chr11:10294486-10294487
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:10294439-10294509	Kidney_OC	kidney:	n/a	n/a
2	CTCF	chr11:10294430-10294547	GM20000	blood:	n/a	n/a

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
ENSG00000254719	TF binding region
ENSG00000148926	Chromatin interaction
ENSG00000254554	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10500722	0.82[AFR][1000 genomes]
rs10500724	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10743131	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10743133	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10770096	0.80[EUR][1000 genomes]
rs10770104	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840381	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10840382	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs10840385	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11042687	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11042702	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11042703	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11042714	0.89[EUR][1000 genomes]
rs11042716	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11042719	0.89[EUR][1000 genomes]
rs11602090	0.80[EUR][1000 genomes]
rs11607174	0.87[EUR][1000 genomes]
rs12279861	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12290748	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12419593	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1442738	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2044143	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2044144	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2083715	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2083716	0.91[EUR][1000 genomes]
rs34051776	0.88[EUR][1000 genomes]
rs34087225	0.88[EUR][1000 genomes]
rs34692066	0.88[EUR][1000 genomes]
rs34739790	0.88[EUR][1000 genomes]
rs35737881	0.87[EUR][1000 genomes]
rs36167833	0.88[EUR][1000 genomes]
rs36170347	0.86[EUR][1000 genomes]
rs4418806	0.83[EUR][1000 genomes]
rs4442543	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4482025	0.80[EUR][1000 genomes]
rs4597056	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4910097	0.84[EUR][1000 genomes]
rs4910107	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4910108	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4910115	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs55933041	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs56063978	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs56776911	0.84[EUR][1000 genomes]
rs6484141	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6484147	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6484148	0.89[EUR][1000 genomes]
rs6484152	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6484160	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7106998	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7107040	0.88[EUR][1000 genomes]
rs7107290	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7107399	0.89[EUR][1000 genomes]
rs7107951	0.88[EUR][1000 genomes]
rs7108358	0.89[EUR][1000 genomes]
rs7110652	0.89[EUR][1000 genomes]
rs7115944	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7116147	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7118500	0.85[EUR][1000 genomes]
rs716803	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs726102	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7479039	0.81[EUR][1000 genomes]
rs7924631	0.82[EUR][1000 genomes]
rs7928170	0.80[EUR][1000 genomes]
rs7938543	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7944706	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7945930	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7947666	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7950461	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7952105	0.89[EUR][1000 genomes]
rs9735682	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv3383912	chr11:10292026-10294824	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
5	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
rs10840380	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	chr11:10294400-10294800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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