Variant report

Variant	rs2439707
Chromosome Location	chr10:90609573-90609574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90599583..90601963-chr10:90608850..90611215,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1008719	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11202897	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs11202898	0.91[CEU][hapmap];1.00[CHD][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs11202899	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs11202902	0.91[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11202906	0.83[CEU][hapmap]
rs11202907	0.83[CEU][hapmap]
rs11591231	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs11596205	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1214564	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12241401	0.86[EUR][1000 genomes]
rs12254084	0.82[CEU][hapmap]
rs12254856	0.91[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12267680	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1411780	1.00[CHD][hapmap]
rs1653842	1.00[CHD][hapmap]
rs17114327	0.82[CEU][hapmap]
rs1769692	1.00[CHD][hapmap]
rs2119685	0.83[CEU][hapmap]
rs2481918	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303525	1.00[CHD][hapmap]
rs303526	1.00[CHD][hapmap]
rs376036	1.00[CHD][hapmap]
rs378308	1.00[CHD][hapmap]
rs390436	1.00[CHD][hapmap]
rs407433	1.00[CHD][hapmap]
rs41284106	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41317244	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs434401	1.00[CHD][hapmap]
rs442545	1.00[CHD][hapmap]
rs451949	1.00[CHD][hapmap]
rs454439	1.00[CHD][hapmap]
rs45493098	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56104559	0.87[EUR][1000 genomes]
rs56228317	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56268252	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57807025	0.87[EUR][1000 genomes]
rs59737591	0.87[EUR][1000 genomes]
rs66478243	0.87[EUR][1000 genomes]
rs7078383	0.83[CEU][hapmap]
rs7085698	0.83[CEU][hapmap]
rs7090631	0.83[CEU][hapmap]
rs7098235	0.83[CEU][hapmap]
rs72809310	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72809311	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72809314	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72809318	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72809335	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72809337	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72809342	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7897521	0.83[CEU][hapmap]
rs7915393	0.83[CEU][hapmap]
rs988584	0.96[AMR][1000 genomes];0.90[EUR][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	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2439707	MYBPC2	trans	lymphoblastoid	seeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90578600-90611200	Weak transcription	Esophagus	oesophagus
2	chr10:90606600-90611400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr10:90606600-90614200	Weak transcription	Gastric	stomach
4	chr10:90606800-90610000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr10:90606800-90611400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr10:90606800-90613200	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr10:90607000-90609600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr10:90607200-90610200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr10:90607600-90611200	Weak transcription	Fetal Intestine Large	intestine
10	chr10:90607600-90612600	Enhancers	Hela-S3	cervix
11	chr10:90608000-90614800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr10:90608200-90609800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr10:90608200-90613400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr10:90608600-90609800	Enhancers	NHDF-Ad	bronchial
15	chr10:90608600-90610000	Enhancers	Sigmoid Colon	Sigmoid Colon
16	chr10:90608600-90611200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr10:90608600-90612400	Weak transcription	Adipose Nuclei	Adipose
18	chr10:90608600-90613000	Enhancers	HMEC	breast
19	chr10:90608800-90609800	Enhancers	Muscle Satellite Cultured Cells	--
20	chr10:90608800-90611200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:90608800-90611600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:90608800-90612800	Enhancers	NHEK	skin
23	chr10:90609000-90611200	Weak transcription	A549	lung
24	chr10:90609000-90611800	Active TSS	Primary B cells from cord blood	blood
25	chr10:90609200-90609600	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr10:90609200-90609600	Flanking Active TSS	Stomach Mucosa	stomach
27	chr10:90609200-90609800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr10:90609200-90609800	Enhancers	Fetal Lung	lung
29	chr10:90609200-90609800	Enhancers	Osteobl	bone
30	chr10:90609200-90610200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr10:90609200-90610200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:90609200-90610200	Weak transcription	GM12878-XiMat	blood
33	chr10:90609200-90610400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr10:90609200-90611000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr10:90609200-90611400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr10:90609200-90611400	Weak transcription	HSMM	muscle
37	chr10:90609400-90609800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr10:90609400-90610200	Weak transcription	Small Intestine	intestine
39	chr10:90609400-90611400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr10:90609400-90611400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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