Variant report

Variant	rs948378
Chromosome Location	chr11:121120845-121120846
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	chr11:121119963..121121540-chr11:121162241..121164433,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109929	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10160458	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10160459	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10160642	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10790413	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10790414	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10790415	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10892696	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10892698	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10892699	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12279833	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1941306	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2105670	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4936597	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6589865	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6589866	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7103283	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7103470	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7115337	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7115463	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7120765	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7129292	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7129508	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7129582	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7928669	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7942167	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs948377	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs948379	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][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	nsv1042295	chr11:121072853-121177079	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
2	nsv898424	chr11:121108865-121206354	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv898425	chr11:121115206-121215237	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs948378	CDA	trans	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:121118200-121121000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:121119600-121121000	Weak transcription	HSMMtube	muscle
3	chr11:121119800-121121200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:121119800-121121200	Enhancers	Liver	Liver
5	chr11:121119800-121122200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:121119800-121122600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:121120000-121121000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:121120000-121121400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr11:121120000-121124400	Weak transcription	NHEK	skin
10	chr11:121120200-121121000	Weak transcription	HMEC	breast
11	chr11:121120200-121121800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
12	chr11:121120200-121122200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr11:121120200-121122400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr11:121120400-121121400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:121120400-121122000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr11:121120400-121122000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr11:121120400-121122200	Enhancers	HSMM	muscle
18	chr11:121120400-121122600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr11:121120600-121121200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr11:121120600-121121800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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