Variant report

Variant	rs12790474
Chromosome Location	chr11:86347981-86347982
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86346719..86349845-chr11:86488350..86491309,3	MCF-7	breast:
2	chr11:86345410..86347094-chr11:86347295..86350272,2	MCF-7	breast:
3	chr11:86346931..86348869-chr11:86351616..86354128,2	K562	blood:
4	chr11:86342318..86349364-chr11:86509780..86514935,13	MCF-7	breast:
5	chr11:86341794..86343569-chr11:86345090..86348008,2	MCF-7	breast:
6	chr11:86346528..86348844-chr11:86457417..86460033,2	MCF-7	breast:
7	chr11:86347212..86349048-chr11:86508932..86511898,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10501627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10501628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898525	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11234707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11234708	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11494278	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11606017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11607554	1.00[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12361283	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12362293	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12365092	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12804997	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1540083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541308	0.82[ASN][1000 genomes]
rs1541309	1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1541310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1938922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382935	1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4944614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930619	1.00[JPT][hapmap]

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	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv555704	chr11:86344677-86386784	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	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
rs12790474	ME3	cis	multi-tissue	Pritchard
rs12790474	CTSC	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86333200-86349800	Weak transcription	Esophagus	oesophagus
2	chr11:86336000-86348000	Weak transcription	Fetal Intestine Small	intestine
3	chr11:86339200-86349200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:86340000-86357200	Weak transcription	Fetal Brain Female	brain
5	chr11:86341000-86349000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr11:86341000-86355400	Weak transcription	Adipose Nuclei	Adipose
7	chr11:86341600-86358800	Weak transcription	Brain Anterior Caudate	brain
8	chr11:86342000-86349200	Weak transcription	Fetal Heart	heart
9	chr11:86342200-86348400	Weak transcription	Left Ventricle	heart
10	chr11:86342200-86348400	Weak transcription	Right Ventricle	heart
11	chr11:86342200-86348800	Weak transcription	Brain Angular Gyrus	brain
12	chr11:86342200-86351400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:86342200-86353200	Weak transcription	Aorta	Aorta
14	chr11:86342200-86356400	Weak transcription	Fetal Stomach	stomach
15	chr11:86343800-86350000	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:86344000-86373800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr11:86344200-86352800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr11:86344400-86348400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:86344400-86349000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:86344600-86354600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:86344800-86348800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr11:86344800-86349000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:86344800-86349000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:86344800-86349000	Weak transcription	NHEK	skin
25	chr11:86344800-86349000	Weak transcription	Osteobl	bone
26	chr11:86344800-86355400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:86344800-86355800	Weak transcription	Pancreas	Pancrea
28	chr11:86345000-86348400	Weak transcription	Spleen	Spleen
29	chr11:86345000-86349400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:86345400-86353000	Weak transcription	HSMM	muscle
31	chr11:86346400-86348400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:86346400-86349200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:86346400-86351200	Weak transcription	Gastric	stomach
34	chr11:86346600-86348000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:86346600-86351800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:86346600-86359600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr11:86346800-86348000	Enhancers	NHDF-Ad	bronchial
38	chr11:86346800-86351200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr11:86347000-86348200	Enhancers	Placenta Amnion	Placenta Amnion
40	chr11:86347000-86349200	Genic enhancers	Ovary	ovary
41	chr11:86347000-86350000	Weak transcription	NH-A	brain
42	chr11:86347200-86348400	Enhancers	A549	lung
43	chr11:86347200-86349200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:86347200-86351600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr11:86347200-86352600	Weak transcription	HUVEC	blood vessel
46	chr11:86347400-86348200	Enhancers	Fetal Kidney	kidney
47	chr11:86347600-86348400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr11:86347800-86348400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:86347800-86348800	Weak transcription	HMEC	breast
50	chr11:86347800-86349000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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