Variant report

Variant	rs11042775
Chromosome Location	chr11:10410316-10410317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:10408455..10411116-chr11:10414237..10415892,3	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10743136	0.96[CEU][hapmap]
rs11042768	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2060659	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28658296	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2923119	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2957661	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7126751	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[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	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	nsv1037131	chr11:10401998-10429998	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv553477	chr11:10403539-10429998	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11042775	SPP1	trans	cerebellum	SCAN
rs11042775	SCG3	trans	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10407200-10410400	Enhancers	Skeletal Muscle Female	skeletal muscle
2	chr11:10407200-10410600	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr11:10407200-10410800	Enhancers	Colon Smooth Muscle	Colon
4	chr11:10407200-10411000	Enhancers	Ovary	ovary
5	chr11:10407200-10411000	Enhancers	NHLF	lung
6	chr11:10407200-10412800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:10407200-10412800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:10407200-10412800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr11:10407200-10412800	Enhancers	Adipose Nuclei	Adipose
10	chr11:10407400-10410400	Enhancers	Rectal Smooth Muscle	rectum
11	chr11:10407400-10411000	Enhancers	Fetal Stomach	stomach
12	chr11:10407800-10412200	Enhancers	NHDF-Ad	bronchial
13	chr11:10408400-10410400	Enhancers	Fetal Lung	lung
14	chr11:10408400-10410600	Enhancers	Esophagus	oesophagus
15	chr11:10408400-10411400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr11:10408600-10410400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:10408600-10413200	Enhancers	Placenta	Placenta
18	chr11:10408800-10410400	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr11:10409000-10410600	Enhancers	Fetal Intestine Small	intestine
20	chr11:10409000-10410800	Enhancers	Muscle Satellite Cultured Cells	--
21	chr11:10409000-10412600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:10409200-10412800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:10409400-10410400	Enhancers	Fetal Kidney	kidney
24	chr11:10409400-10411000	Enhancers	Lung	lung
25	chr11:10409400-10412000	Weak transcription	Brain Hippocampus Middle	brain
26	chr11:10409600-10412200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:10409600-10412800	Enhancers	Osteobl	bone
28	chr11:10409600-10413800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr11:10409600-10420000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:10409600-10420000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr11:10409800-10410400	Enhancers	Fetal Muscle Trunk	muscle
32	chr11:10409800-10414000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:10410000-10412800	Enhancers	Stomach Smooth Muscle	stomach
34	chr11:10410000-10413800	Weak transcription	NH-A	brain
35	chr11:10410200-10410400	Weak transcription	Right Atrium	heart
36	chr11:10410200-10411400	Weak transcription	A549	lung
37	chr11:10410200-10412000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:10410200-10412000	Weak transcription	Duodenum Smooth Muscle	Duodenum

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