Variant report

Variant	rs17726706
Chromosome Location	chr11:47476377-47476378
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47475921..47477972-chr11:47598148..47600400,2	MCF-7	breast:
2	chr11:47394123..47395677-chr11:47474242..47477201,2	MCF-7	breast:
3	chr11:47475878..47478191-chr11:47478977..47480771,2	K562	blood:
4	chr11:47395073..47396141-chr11:47475486..47476579,4	MCF-7	breast:
5	chr11:47446237..47448269-chr11:47475796..47477520,2	MCF-7	breast:
6	chr11:47376825..47377467-chr11:47475964..47476482,2	MCF-7	breast:
7	chr11:47446223..47447873-chr11:47474244..47476501,2	MCF-7	breast:
8	chr11:47476020..47478191-chr11:47478977..47481555,2	K562	blood:
9	chr11:47475117..47477912-chr11:47481556..47483873,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000165916	Chromatin interaction
ENSG00000123444	Chromatin interaction
ENSG00000231880	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11570058	0.91[CEU][hapmap]
rs11570067	0.91[CEU][hapmap]
rs12285933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17726787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3729989	0.91[CEU][hapmap]
rs3736101	0.81[CEU][hapmap]
rs3816724	0.81[CEU][hapmap]
rs45547231	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45603036	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45617144	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56007045	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57680742	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895077	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895081	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895102	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61895104	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61895111	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61895113	0.89[ASN][1000 genomes]
rs61897390	0.80[EUR][1000 genomes]
rs61897391	0.82[EUR][1000 genomes]
rs61897423	0.83[ASN][1000 genomes]
rs61897424	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61897426	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897429	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897430	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61897432	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897434	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7104800	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7108608	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7116534	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919527	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919657	0.86[EUR][1000 genomes];1.00[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	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
2	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17726706	PSMC3	cis	parietal	SCAN
rs17726706	PSMC3	cis	cerebellum	SCAN
rs17726706	MTCH2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47448600-47488400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:47453400-47480000	Weak transcription	Thymus	Thymus
3	chr11:47457400-47480200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:47457400-47480800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:47457400-47488400	Weak transcription	Gastric	stomach
6	chr11:47459800-47480600	Weak transcription	Fetal Intestine Small	intestine
7	chr11:47459800-47480800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:47461800-47480800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:47464000-47481000	Weak transcription	NHEK	skin
10	chr11:47465000-47480800	Weak transcription	Adipose Nuclei	Adipose
11	chr11:47465800-47480800	Weak transcription	Primary T cells from cord blood	blood
12	chr11:47468800-47482200	Weak transcription	HUVEC	blood vessel
13	chr11:47471000-47480800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:47471000-47480800	Weak transcription	Left Ventricle	heart
15	chr11:47471000-47480800	Weak transcription	Pancreas	Pancrea
16	chr11:47471000-47486200	Weak transcription	Right Ventricle	heart
17	chr11:47471200-47482200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:47471200-47488400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr11:47471400-47479600	Weak transcription	Placenta	Placenta
20	chr11:47471400-47480600	Weak transcription	A549	lung
21	chr11:47471400-47480800	Weak transcription	Lung	lung
22	chr11:47471400-47489200	Weak transcription	HepG2	liver
23	chr11:47471600-47480600	Weak transcription	HSMM	muscle
24	chr11:47471600-47480600	Weak transcription	HSMMtube	muscle
25	chr11:47471600-47480800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:47471600-47486000	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr11:47471800-47476400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:47471800-47485600	Weak transcription	Spleen	Spleen
29	chr11:47472000-47485600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:47474000-47485800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:47474600-47480800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr11:47475000-47480600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:47475200-47482600	Weak transcription	NH-A	brain
34	chr11:47475400-47479800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr11:47475400-47480200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:47475600-47476400	Enhancers	K562	blood
37	chr11:47475600-47476600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr11:47475800-47476600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:47475800-47480800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:47475800-47480800	Weak transcription	NHLF	lung
41	chr11:47475800-47482200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:47475800-47486800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:47476000-47476600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr11:47476000-47477200	Weak transcription	Liver	Liver
45	chr11:47476000-47480200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr11:47476000-47480200	Weak transcription	Fetal Muscle Leg	muscle
47	chr11:47476000-47480800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:47476000-47483600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr11:47476000-47486800	Weak transcription	Colon Smooth Muscle	Colon
50	chr11:47476000-47487400	Weak transcription	Brain Cingulate Gyrus	brain

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