Variant report

Variant	rs3740689
Chromosome Location	chr11:47380593-47380594
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47372212..47375004-chr11:47380040..47382047,2	MCF-7	breast:
2	chr11:47380057..47381801-chr11:47388110..47390294,2	K562	blood:
3	chr11:47379032..47381068-chr11:47385092..47386815,2	MCF-7	breast:
4	chr11:47195702..47198669-chr11:47379540..47381275,2	K562	blood:
5	chr11:47380338..47382124-chr11:47391375..47394972,3	K562	blood:

Variant related genes	Relation type
ENSG00000134571	Chromatin interaction
ENSG00000149182	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10769264	0.83[CHB][hapmap]
rs10838709	0.83[CHB][hapmap]
rs11039225	0.83[CHB][hapmap]
rs11039244	0.83[CHB][hapmap]
rs11604680	1.00[YRI][hapmap]
rs12292911	0.83[CHB][hapmap]
rs2293576	0.83[CHB][hapmap]
rs34958982	0.94[LWK][hapmap]
rs6485758	0.83[CHB][hapmap]
rs7103648	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv3439899	chr11:47376276-47381174	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	esv3440608	chr11:47379026-47381524	Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised 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	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3740689	PSMC3	cis	parietal	SCAN
rs3740689	MADD	cis	parietal	SCAN
rs3740689	PSMC3	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47375400-47381000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr11:47375600-47380600	Strong transcription	Primary B cells from cord blood	blood
3	chr11:47375600-47381000	Strong transcription	Primary B cells from peripheral blood	blood
4	chr11:47376800-47381400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:47377200-47386600	Weak transcription	Right Atrium	heart
6	chr11:47377200-47391400	Weak transcription	Psoas Muscle	Psoas
7	chr11:47377200-47397800	Weak transcription	Fetal Muscle Leg	muscle
8	chr11:47377600-47380800	Weak transcription	Brain Hippocampus Middle	brain
9	chr11:47377600-47381000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr11:47377600-47381000	Weak transcription	Placenta	Placenta
11	chr11:47377600-47396800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:47377600-47397600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:47377600-47397800	Weak transcription	Brain Substantia Nigra	brain
14	chr11:47377800-47380800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr11:47377800-47382200	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:47377800-47382600	Weak transcription	Fetal Heart	heart
17	chr11:47377800-47382800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:47378000-47381400	Weak transcription	Colonic Mucosa	Colon
19	chr11:47378400-47381400	Weak transcription	Fetal Intestine Small	intestine
20	chr11:47378600-47381400	Weak transcription	Pancreas	Pancrea
21	chr11:47378600-47382000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:47378800-47381600	Weak transcription	Fetal Lung	lung
23	chr11:47378800-47381800	Weak transcription	Adipose Nuclei	Adipose
24	chr11:47378800-47393400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr11:47379600-47381000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr11:47379800-47380600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
27	chr11:47379800-47380800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:47379800-47382000	Genic enhancers	Spleen	Spleen
29	chr11:47380000-47380600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
30	chr11:47380000-47382000	Enhancers	Right Ventricle	heart
31	chr11:47380000-47397800	Weak transcription	Esophagus	oesophagus
32	chr11:47380200-47380600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr11:47380200-47380600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:47380200-47380800	Bivalent Enhancer	HepG2	liver
35	chr11:47380200-47381000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr11:47380200-47381000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr11:47380200-47383600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr11:47380200-47395200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr11:47380200-47396600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr11:47380200-47397200	Weak transcription	Brain Anterior Caudate	brain
41	chr11:47380200-47397800	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:47380400-47380800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:47380400-47381000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:47380400-47381200	Genic enhancers	Monocytes-CD14+_RO01746	blood
45	chr11:47380400-47382800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:47380400-47382800	Weak transcription	GM12878-XiMat	blood
47	chr11:47380400-47383600	Enhancers	Dnd41	blood
48	chr11:47380400-47389000	Genic enhancers	Primary monocytes fromperipheralblood	blood
49	chr11:47380400-47397000	Weak transcription	Lung	lung

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