Variant report

Variant	rs4980506
Chromosome Location	chr11:63878350-63878351
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63845669..63847222-chr11:63878087..63880770,2	MCF-7	breast:
2	chr11:63753024..63754792-chr11:63877505..63880384,2	MCF-7	breast:
3	chr11:63871394..63875273-chr11:63876686..63880197,5	K562	blood:

Variant related genes	Relation type
ENSG00000167770	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11549691	0.81[EUR][1000 genomes]
rs1544538	0.85[EUR][1000 genomes]
rs17851033	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1938817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2070232	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2154984	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2186571	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2245837	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2622420	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2622422	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2622424	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2622428	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2622430	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2701530	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2701536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2701537	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2701539	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs583799	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59250939	0.85[EUR][1000 genomes]
rs599549	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs615924	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs616652	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs639406	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs688241	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
3	esv1849906	chr11:63719273-63880383	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
5	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
6	nsv832184	chr11:63787702-63925084	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	234 gene(s)	inside rSNPs	diseases
8	nsv897658	chr11:63810944-63897759	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv897659	chr11:63813470-63907079	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
11	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
12	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
13	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
14	nsv356	chr11:63868847-63913129	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	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
rs4980506	PRDX5	Cis_1M	lymphoblastoid	RTeQTL
rs4980506	HSPC152	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63866000-63878800	Weak transcription	Esophagus	oesophagus
2	chr11:63866400-63887800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:63867000-63882800	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:63867400-63878400	Weak transcription	HepG2	liver
5	chr11:63869600-63878400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr11:63870000-63879400	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr11:63870000-63884400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:63871200-63884200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:63871400-63881000	Weak transcription	Gastric	stomach
10	chr11:63872200-63882400	Weak transcription	Fetal Brain Female	brain
11	chr11:63872800-63883600	Weak transcription	Pancreas	Pancrea
12	chr11:63873400-63886800	Weak transcription	Colonic Mucosa	Colon
13	chr11:63873800-63878600	Weak transcription	Left Ventricle	heart
14	chr11:63873800-63884200	Weak transcription	Brain Anterior Caudate	brain
15	chr11:63874000-63884200	Weak transcription	Brain Angular Gyrus	brain
16	chr11:63874200-63880000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr11:63874200-63881200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr11:63874200-63882800	Weak transcription	Fetal Stomach	stomach
19	chr11:63874200-63883400	Weak transcription	Brain Hippocampus Middle	brain
20	chr11:63874200-63883800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:63874200-63883800	Weak transcription	Brain Substantia Nigra	brain
22	chr11:63875400-63878400	Weak transcription	Brain Germinal Matrix	brain
23	chr11:63875400-63878800	Weak transcription	Fetal Muscle Leg	muscle
24	chr11:63875400-63880800	Weak transcription	Hela-S3	cervix
25	chr11:63875400-63883000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:63875400-63896200	Weak transcription	Spleen	Spleen
27	chr11:63875600-63886800	Weak transcription	HSMMtube	muscle
28	chr11:63876200-63884200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:63876400-63879400	Enhancers	Right Ventricle	heart
30	chr11:63877200-63881200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr11:63877400-63878400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:63877400-63878600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:63877400-63878600	Weak transcription	Fetal Intestine Small	intestine
34	chr11:63877400-63882800	Weak transcription	Fetal Heart	heart
35	chr11:63877400-63883800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:63878000-63879400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr11:63878000-63879600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:63878200-63878400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr11:63878200-63878400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr11:63878200-63878600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr11:63878200-63880800	Weak transcription	Lung	lung

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