Variant report

Variant	rs4459318
Chromosome Location	chr11:119541778-119541779
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	chr11:119540900..119542857-chr11:119592650..119594796,2	MCF-7	breast:
2	chr11:119536475..119542158-chr11:119597745..119601129,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110400	Chromatin interaction
ENSG00000254854	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10790330	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10790331	0.86[EUR][1000 genomes]
rs10790332	0.88[GIH][hapmap];0.85[TSI][hapmap]
rs2292293	0.88[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs4936492	0.80[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs4938704	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4938705	0.91[EUR][1000 genomes]
rs4938706	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4938708	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs4938709	0.82[EUR][1000 genomes]
rs4938711	0.82[JPT][hapmap]
rs7118532	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7933848	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs7950059	0.85[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes]
rs906830	0.88[GIH][hapmap];0.85[TSI][hapmap]

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	nsv898421	chr11:119499014-119631325	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv984471	chr11:119505802-119568473	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv898422	chr11:119518006-119601779	Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv898423	chr11:119541332-119659753	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4459318	UPK2	cis	cerebellum	SCAN
rs4459318	RPS25	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119523200-119541800	Weak transcription	Left Ventricle	heart
2	chr11:119530200-119546000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:119531000-119542000	Weak transcription	Colonic Mucosa	Colon
4	chr11:119531200-119541800	Weak transcription	Fetal Heart	heart
5	chr11:119532400-119544400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr11:119532800-119541800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:119533000-119542000	Weak transcription	Right Atrium	heart
8	chr11:119533000-119543400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:119534800-119542600	Weak transcription	Fetal Kidney	kidney
10	chr11:119535000-119542000	Weak transcription	Fetal Thymus	thymus
11	chr11:119535000-119542400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:119535200-119542200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr11:119535200-119542400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:119535200-119542600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:119535200-119544200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:119535200-119552600	Weak transcription	HepG2	liver
17	chr11:119536000-119544000	Weak transcription	Fetal Intestine Large	intestine
18	chr11:119536200-119541800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:119536400-119542600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:119536400-119544000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:119537000-119541800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:119537000-119541800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr11:119537000-119541800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr11:119537000-119542400	Weak transcription	Spleen	Spleen
25	chr11:119537000-119542800	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr11:119537400-119541800	Weak transcription	Osteobl	bone
27	chr11:119537600-119541800	Weak transcription	Adipose Nuclei	Adipose
28	chr11:119537600-119541800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:119537600-119542000	Weak transcription	Liver	Liver
30	chr11:119537600-119542200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:119537600-119542200	Weak transcription	Stomach Mucosa	stomach
32	chr11:119537600-119542400	Weak transcription	Pancreas	Pancrea
33	chr11:119537600-119542600	Weak transcription	Gastric	stomach
34	chr11:119537600-119544200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:119537800-119541800	Weak transcription	Ovary	ovary
36	chr11:119537800-119542000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:119537800-119542000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:119537800-119542000	Weak transcription	HMEC	breast
39	chr11:119537800-119542000	Strong transcription	NHEK	skin
40	chr11:119537800-119542200	Weak transcription	Right Ventricle	heart
41	chr11:119537800-119547000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr11:119538000-119542000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:119538200-119541800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:119538200-119542000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:119538400-119541800	Weak transcription	Fetal Brain Female	brain
46	chr11:119538400-119542400	Weak transcription	Primary B cells from cord blood	blood
47	chr11:119538800-119541800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr11:119539000-119542600	Weak transcription	GM12878-XiMat	blood
49	chr11:119539200-119542600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr11:119539400-119541800	Weak transcription	Brain Angular Gyrus	brain

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