Variant report

Variant	rs11088455
Chromosome Location	chr21:40283267-40283268
allele	C/T
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40179122..40182032-chr21:40282581..40284281,2	MCF-7	breast:
2	chr21:40157809..40160879-chr21:40282729..40285436,3	MCF-7	breast:
3	chr21:40282678..40285377-chr21:40330917..40333289,2	MCF-7	breast:
4	chr21:40268571..40270623-chr21:40281221..40283550,2	MCF-7	breast:
5	chr21:40207571..40212513-chr21:40281866..40285274,6	MCF-7	breast:
6	chr21:40188542..40191165-chr21:40281236..40284750,4	MCF-7	breast:
7	chr21:40184223..40185777-chr21:40281184..40284011,2	K562	blood:
8	chr21:40281296..40284388-chr21:40304132..40307612,3	MCF-7	breast:
9	chr21:38935711..38937923-chr21:40282056..40283884,2	MCF-7	breast:
10	chr21:40282115..40285286-chr21:40361301..40363666,3	MCF-7	breast:
11	chr21:40281039..40283900-chr21:40466171..40469070,3	MCF-7	breast:
12	chr21:40268536..40271467-chr21:40282576..40285415,2	K562	blood:
13	chr21:40282471..40284142-chr21:40462594..40465543,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12626608	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62219886	0.81[EUR][1000 genomes]
rs9979503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv587479	chr21:40282556-40297536	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11088455	PSMG1	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40273800-40284800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr21:40277800-40287000	Enhancers	Left Ventricle	heart
3	chr21:40278000-40283400	Enhancers	Placenta	Placenta
4	chr21:40278400-40284800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr21:40278600-40283600	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr21:40278600-40284600	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr21:40278600-40284800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr21:40278600-40285000	Enhancers	NHEK	skin
9	chr21:40278600-40285200	Enhancers	Right Ventricle	heart
10	chr21:40278800-40284400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr21:40279400-40284800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr21:40279600-40283400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr21:40279600-40285600	Weak transcription	Fetal Kidney	kidney
14	chr21:40279800-40285000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr21:40279800-40285600	Weak transcription	NHDF-Ad	bronchial
16	chr21:40280000-40284000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr21:40280200-40284600	Weak transcription	Colon Smooth Muscle	Colon
18	chr21:40280200-40286800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr21:40280400-40284800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr21:40280400-40287200	Enhancers	Esophagus	oesophagus
21	chr21:40280600-40286000	Enhancers	Lung	lung
22	chr21:40280800-40285600	Weak transcription	Aorta	Aorta
23	chr21:40281200-40284000	Flanking Active TSS	Hela-S3	cervix
24	chr21:40281200-40284800	Enhancers	Duodenum Mucosa	Duodenum
25	chr21:40281200-40285000	Enhancers	Stomach Mucosa	stomach
26	chr21:40281400-40284800	Weak transcription	Ovary	ovary
27	chr21:40281400-40284800	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr21:40281400-40286200	Weak transcription	Gastric	stomach
29	chr21:40282000-40283600	Enhancers	Adipose Nuclei	Adipose
30	chr21:40282200-40284400	Weak transcription	Fetal Lung	lung
31	chr21:40282200-40284600	Weak transcription	Colonic Mucosa	Colon
32	chr21:40282200-40285000	Enhancers	HMEC	breast
33	chr21:40282400-40284000	Weak transcription	Fetal Intestine Large	intestine
34	chr21:40282400-40284800	Weak transcription	HUVEC	blood vessel
35	chr21:40282600-40283400	Enhancers	Stomach Smooth Muscle	stomach
36	chr21:40282600-40284000	Weak transcription	Pancreas	Pancrea
37	chr21:40282600-40284000	Weak transcription	HepG2	liver
38	chr21:40282600-40284200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr21:40282600-40284600	Enhancers	Liver	Liver
40	chr21:40282600-40284800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr21:40282600-40284800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr21:40282600-40284800	Weak transcription	Spleen	Spleen
43	chr21:40282600-40287200	Enhancers	Psoas Muscle	Psoas
44	chr21:40282800-40283800	Weak transcription	Small Intestine	intestine
45	chr21:40282800-40284000	Weak transcription	Right Atrium	heart
46	chr21:40282800-40284000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr21:40282800-40284800	Weak transcription	Fetal Muscle Leg	muscle
48	chr21:40282800-40284800	Weak transcription	HSMMtube	muscle
49	chr21:40283000-40284000	Weak transcription	Fetal Intestine Small	intestine
50	chr21:40283000-40284800	Weak transcription	Fetal Heart	heart

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