Variant report

Variant	rs10742298
Chromosome Location	chr11:33662206-33662207
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:33654474..33658649-chr11:33659750..33663424,5	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1033542	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1033543	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1073655	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742299	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10742300	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742301	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10768013	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10836087	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10836088	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1104742	0.83[YRI][hapmap]
rs1569763	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4755237	0.81[AMR][1000 genomes]
rs7106651	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7115033	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7117579	0.91[ASN][1000 genomes]
rs761435	0.82[YRI][hapmap]
rs7949170	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869418	chr11:33053073-33662479	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv832112	chr11:33469782-33683052	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv832113	chr11:33609202-33767781	Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10742298	C11orf41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:33640600-33666400	Weak transcription	Brain Germinal Matrix	brain
2	chr11:33640800-33673600	Weak transcription	Fetal Brain Male	brain
3	chr11:33642600-33673600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:33643000-33673600	Weak transcription	Brain Angular Gyrus	brain
5	chr11:33654200-33666400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:33654200-33666600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:33656000-33667200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:33656200-33667200	Weak transcription	Fetal Brain Female	brain
9	chr11:33656800-33667000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:33656800-33673600	Weak transcription	NH-A	brain
11	chr11:33657400-33673600	Weak transcription	HSMMtube	muscle
12	chr11:33657800-33673600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:33657800-33688400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr11:33658400-33662800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr11:33658600-33667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:33658600-33667600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:33659200-33666400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:33659400-33663400	Weak transcription	HMEC	breast
19	chr11:33659600-33663600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:33662000-33662600	Enhancers	Left Ventricle	heart
21	chr11:33662200-33662600	Weak transcription	Right Atrium	heart
22	chr11:33662200-33667200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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